Correlation between copy number variation genes (focal events) and selected clinical features
Prostate Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1W66K7N
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1W66K7N
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 63 focal events and 11 clinical features across 492 patients, 337 significant findings detected with Q value < 0.25.

  • amp_1q22 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'HISTOLOGICAL_TYPE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • amp_3q21.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • amp_3q26.2 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • amp_4p16.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE', and 'GLEASON_SCORE'.

  • amp_4q13.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • amp_5q35.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • amp_7p14.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'RESIDUAL_TUMOR', and 'GLEASON_SCORE'.

  • amp_7q22.1 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'RESIDUAL_TUMOR', and 'GLEASON_SCORE'.

  • amp_8p11.23 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'RESIDUAL_TUMOR', and 'GLEASON_SCORE'.

  • amp_8q22.1 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • amp_8q24.21 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • amp_9q33.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • amp_11q13.2 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • amp_12q23.1 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • amp_13q12.11 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • amp_14q21.1 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • amp_15q11.2 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • amp_16q11.2 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • amp_17p11.2 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • amp_17q23.2 cnv correlated to 'Time to Death',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'HISTOLOGICAL_TYPE',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • amp_18q21.31 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'GLEASON_SCORE'.

  • amp_19q13.43 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • amp_20q13.2 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • amp_xp22.2 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • amp_xq12 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • amp_xq21.1 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'RACE'.

  • amp_xq21.31 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'RESIDUAL_TUMOR',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • amp_xq25 cnv correlated to 'PATHOLOGY_T_STAGE',  'GLEASON_SCORE', and 'RACE'.

  • del_1p31.3 cnv correlated to 'PATHOLOGY_T_STAGE',  'RADIATION_THERAPY',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • del_1p22.1 cnv correlated to 'PATHOLOGY_T_STAGE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • del_1q42.3 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RESIDUAL_TUMOR',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • del_2p21 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • del_2q22.1 cnv correlated to 'YEARS_TO_BIRTH' and 'GLEASON_SCORE'.

  • del_2q22.3 cnv correlated to 'YEARS_TO_BIRTH' and 'GLEASON_SCORE'.

  • del_3p13 cnv correlated to 'YEARS_TO_BIRTH' and 'RADIATION_THERAPY'.

  • del_3q29 cnv correlated to 'GLEASON_SCORE'.

  • del_4q28.2 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'RADIATION_THERAPY', and 'GLEASON_SCORE'.

  • del_5q11.2 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • del_5q13.2 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • del_5q21.1 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • del_6p25.1 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'RACE'.

  • del_6q14.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • del_8p21.3 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • del_9p23 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • del_10q23.31 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • del_11p11.2 cnv correlated to 'PATHOLOGY_T_STAGE',  'RESIDUAL_TUMOR',  'GLEASON_SCORE', and 'RACE'.

  • del_11q22.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'RADIATION_THERAPY',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • del_11q23.2 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'RADIATION_THERAPY',  'RESIDUAL_TUMOR', and 'GLEASON_SCORE'.

  • del_12p13.1 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • del_12q24.32 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • del_13q14.13 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'RADIATION_THERAPY',  'RESIDUAL_TUMOR',  'GLEASON_SCORE', and 'RACE'.

  • del_13q22.1 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'RACE'.

  • del_15q21.3 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • del_16q22.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • del_16q24.1 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • del_17p13.1 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • del_17q21.31 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_18q21.31 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • del_18q23 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • del_19q13.2 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'RESIDUAL_TUMOR', and 'GLEASON_SCORE'.

  • del_21q22.2 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'NUMBER_OF_LYMPH_NODES',  'GLEASON_SCORE', and 'RACE'.

  • del_21q22.3 cnv correlated to 'PATHOLOGY_T_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 63 focal events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 337 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		RESIDUAL
TUMOR 		NUMBER
OF
LYMPH
NODES 		GLEASON
SCORE 		PSA
VALUE 		RACE
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Wilcoxon-test Fisher's exact test
amp 1q22 40 (8%) 452 0.427
(0.601) 		0.0107
(0.0405) 		1e-05
(0.000147) 		0.00116
(0.00697) 		0.0382
(0.106) 		0.0207
(0.0674) 		0.0334
(0.0965) 		6.66e-05
(0.000796) 		1.53e-07
(5.58e-06) 		0.183
(0.346) 		1
(1.00)
amp 8q22 1 157 (32%) 335 0.56
(0.703) 		0.0851
(0.187) 		1e-05
(0.000147) 		0.00215
(0.0111) 		0.0151
(0.0526) 		0.564
(0.704) 		3e-05
(4e-04) 		0.000321
(0.00268) 		1.45e-13
(1.01e-10) 		0.0555
(0.139) 		1
(1.00)
amp 8q24 21 152 (31%) 340 0.969
(1.00) 		0.053
(0.135) 		1e-05
(0.000147) 		0.000759
(0.00496) 		0.0468
(0.123) 		0.565
(0.704) 		0.00014
(0.00139) 		9.4e-05
(0.001) 		9.12e-13
(2.11e-10) 		0.0294
(0.0868) 		0.813
(0.916)
amp 12q23 1 36 (7%) 456 0.473
(0.64) 		0.077
(0.174) 		0.00032
(0.00268) 		0.00127
(0.00746) 		0.0433
(0.116) 		0.273
(0.457) 		0.00029
(0.00254) 		0.000371
(0.00296) 		3.01e-06
(8.03e-05) 		0.0708
(0.167) 		1
(1.00)
amp 15q11 2 16 (3%) 476 0.0849
(0.187) 		0.0738
(0.169) 		0.109
(0.232) 		0.000298
(0.00258) 		0.0772
(0.174) 		1
(1.00) 		0.0142
(0.0502) 		9.6e-07
(3.02e-05) 		0.00139
(0.00799) 		0.56
(0.703)
amp 16q11 2 30 (6%) 462 0.508
(0.66) 		0.0266
(0.0819) 		0.00025
(0.00231) 		0.0724
(0.167) 		0.102
(0.22) 		0.208
(0.376) 		0.0388
(0.107) 		0.0631
(0.154) 		1.71e-06
(5.14e-05) 		0.0183
(0.061) 		1
(1.00)
amp 17q23 2 25 (5%) 467 0.115
(0.24) 		0.172
(0.329) 		0.00091
(0.00574) 		0.0216
(0.07) 		0.0547
(0.138) 		0.0291
(0.0867) 		0.201
(0.367) 		0.012
(0.0438) 		7.54e-05
(0.000857) 		0.0468
(0.123) 		1
(1.00)
amp 20q13 2 45 (9%) 447 0.988
(1.00) 		0.00432
(0.0189) 		1e-05
(0.000147) 		0.00992
(0.0376) 		0.0832
(0.184) 		0.372
(0.558) 		0.012
(0.0438) 		0.00157
(0.00884) 		7.21e-08
(2.94e-06) 		0.073
(0.167) 		1
(1.00)
del 13q22 1 176 (36%) 316 0.304
(0.481) 		0.000926
(0.00574) 		0.00021
(0.00199) 		0.0921
(0.2) 		0.112
(0.236) 		0.397
(0.578) 		0.0132
(0.0473) 		0.0445
(0.118) 		3.04e-10
(3.51e-08) 		0.261
(0.44) 		0.0004
(0.00311)
amp 3q21 3 75 (15%) 417 0.191
(0.357) 		0.00251
(0.0127) 		1e-05
(0.000147) 		0.00207
(0.0109) 		0.0431
(0.116) 		0.246
(0.421) 		0.0005
(0.0035) 		5.13e-05
(0.000647) 		3.56e-11
(6.16e-09) 		0.144
(0.284) 		0.661
(0.791)
amp 3q26 2 86 (17%) 406 0.274
(0.458) 		0.0225
(0.0719) 		1e-05
(0.000147) 		0.000717
(0.00473) 		0.13
(0.263) 		0.281
(0.464) 		0.00014
(0.00139) 		2.93e-05
(0.000398) 		1.18e-09
(9.97e-08) 		0.0539
(0.137) 		1
(1.00)
amp 9q33 3 62 (13%) 430 0.896
(0.992) 		0.0246
(0.0775) 		1e-05
(0.000147) 		1.87e-08
(8.64e-07) 		0.203
(0.371) 		0.0865
(0.189) 		0.00038
(0.00299) 		9.81e-11
(1.36e-08) 		6.13e-13
(2.11e-10) 		0.245
(0.421) 		0.557
(0.702)
amp 19q13 43 19 (4%) 473 0.224
(0.396) 		0.0263
(0.0819) 		0.00035
(0.00282) 		0.0304
(0.0888) 		1
(1.00) 		0.0975
(0.211) 		0.12
(0.247) 		0.00407
(0.0184) 		3.73e-06
(9.23e-05) 		0.509
(0.66) 		1
(1.00)
amp xp22 2 27 (5%) 465 0.555
(0.702) 		0.016
(0.0555) 		0.00179
(0.00965) 		0.0359
(0.102) 		0.175
(0.333) 		0.176
(0.333) 		0.00092
(0.00574) 		0.00664
(0.0272) 		4.75e-05
(0.00061) 		0.0709
(0.167) 		0.165
(0.317)
amp xq21 1 14 (3%) 478 0.594
(0.727) 		0.0164
(0.0557) 		0.0194
(0.0637) 		0.0274
(0.0831) 		0.705
(0.833) 		1
(1.00) 		0.0785
(0.177) 		0.027
(0.0824) 		0.00216
(0.0111) 		0.364
(0.553) 		0.0274
(0.0831)
del 5q11 2 105 (21%) 387 0.7
(0.831) 		0.0429
(0.116) 		1e-05
(0.000147) 		0.000458
(0.00336) 		0.0266
(0.0819) 		0.744
(0.866) 		0.0363
(0.102) 		8.86e-06
(0.000147) 		1.22e-09
(9.97e-08) 		0.592
(0.727) 		0.461
(0.633)
del 16q22 3 191 (39%) 301 0.423
(0.597) 		0.039
(0.107) 		0.00033
(0.00272) 		0.0294
(0.0868) 		0.775
(0.887) 		1
(1.00) 		0.0284
(0.0856) 		0.00793
(0.0314) 		4.97e-09
(3.13e-07) 		0.114
(0.24) 		0.717
(0.846)
amp 4q13 3 22 (4%) 470 0.539
(0.69) 		0.0193
(0.0636) 		0.00193
(0.0102) 		0.00051
(0.0035) 		0.295
(0.471) 		0.478
(0.641) 		0.00526
(0.0224) 		5.9e-05
(0.000718) 		0.000271
(0.00245) 		0.366
(0.553) 		1
(1.00)
amp 5q35 3 28 (6%) 464 0.46
(0.632) 		2.58e-07
(8.94e-06) 		0.00022
(0.00206) 		0.000701
(0.00467) 		0.556
(0.702) 		0.565
(0.704) 		0.0658
(0.158) 		7.33e-05
(0.000857) 		3.95e-05
(0.000516) 		0.951
(1.00) 		0.262
(0.441)
amp 11q13 2 48 (10%) 444 0.418
(0.594) 		0.0005
(0.0035) 		2e-05
(0.000277) 		9.47e-06
(0.000147) 		0.15
(0.291) 		0.637
(0.768) 		0.00161
(0.00893) 		9.95e-08
(3.83e-06) 		1.09e-08
(5.41e-07) 		0.611
(0.746) 		0.347
(0.535)
amp 14q21 1 30 (6%) 462 0.681
(0.809) 		0.0372
(0.104) 		0.0694
(0.165) 		0.0147
(0.0516) 		0.00329
(0.0155) 		0.208
(0.376) 		0.413
(0.593) 		0.00605
(0.0251) 		8.39e-05
(0.000938) 		0.897
(0.992) 		1
(1.00)
amp xq12 16 (3%) 476 0.12
(0.247) 		0.00298
(0.0143) 		0.00745
(0.0297) 		0.149
(0.291) 		0.43
(0.604) 		1
(1.00) 		0.0128
(0.0464) 		0.0298
(0.0876) 		7.7e-06
(0.000147) 		0.281
(0.464)
del 6q14 3 180 (37%) 312 0.317
(0.498) 		0.000954
(0.00585) 		0.0636
(0.155) 		0.0268
(0.0822) 		0.191
(0.357) 		1
(1.00) 		0.00045
(0.00335) 		0.0135
(0.0481) 		0.000342
(0.00279) 		0.539
(0.69) 		0.585
(0.721)
del 8p21 3 294 (60%) 198 0.4
(0.581) 		0.378
(0.563) 		1e-05
(0.000147) 		0.00273
(0.0134) 		0.0639
(0.155) 		0.582
(0.72) 		0.13
(0.263) 		0.00105
(0.00638) 		0.000927
(0.00574) 		0.0683
(0.164) 		0.729
(0.857)
del 10q23 31 157 (32%) 335 0.879
(0.981) 		0.53
(0.682) 		1e-05
(0.000147) 		0.00352
(0.0163) 		0.0258
(0.0809) 		0.775
(0.887) 		0.124
(0.254) 		0.00081
(0.0052) 		3.5e-08
(1.52e-06) 		0.00845
(0.0331) 		0.234
(0.411)
del 11q22 3 43 (9%) 449 0.387
(0.573) 		0.0342
(0.098) 		0.00067
(0.00455) 		0.173
(0.33) 		0.0606
(0.149) 		0.35
(0.539) 		0.00654
(0.027) 		0.0726
(0.167) 		7.51e-05
(0.000857) 		0.786
(0.895) 		0.634
(0.765)
del 12p13 1 124 (25%) 368 0.806
(0.912) 		0.795
(0.901) 		1e-05
(0.000147) 		0.0109
(0.0408) 		0.0358
(0.102) 		0.128
(0.261) 		0.391
(0.575) 		0.00366
(0.0168) 		5.32e-05
(0.000658) 		0.0179
(0.0598) 		1
(1.00)
del 13q14 13 227 (46%) 265 0.895
(0.992) 		0.0136
(0.0484) 		0.00558
(0.0234) 		0.208
(0.376) 		0.00122
(0.00727) 		0.277
(0.461) 		0.00224
(0.0114) 		0.21
(0.377) 		1.97e-05
(0.000277) 		0.281
(0.464) 		0.00409
(0.0184)
del 15q21 3 67 (14%) 425 0.587
(0.723) 		0.277
(0.461) 		1e-05
(0.000147) 		0.00178
(0.00965) 		0.0067
(0.0273) 		0.42
(0.595) 		0.148
(0.29) 		0.000302
(0.00259) 		8.97e-09
(4.78e-07) 		0.121
(0.25) 		1
(1.00)
del 16q24 1 213 (43%) 279 0.418
(0.594) 		0.242
(0.418) 		1e-05
(0.000147) 		0.043
(0.116) 		0.674
(0.802) 		1
(1.00) 		0.109
(0.232) 		0.0164
(0.0557) 		2.12e-09
(1.47e-07) 		0.0798
(0.179) 		1
(1.00)
del 17p13 1 163 (33%) 329 0.548
(0.696) 		0.397
(0.578) 		1e-05
(0.000147) 		0.00359
(0.0166) 		0.0176
(0.0595) 		0.782
(0.893) 		0.0113
(0.0417) 		0.000285
(0.00253) 		1.3e-09
(9.97e-08) 		0.222
(0.394) 		0.822
(0.925)
del 18q21 31 131 (27%) 361 0.455
(0.63) 		0.739
(0.865) 		0.00046
(0.00336) 		0.0244
(0.0773) 		0.111
(0.236) 		0.769
(0.885) 		0.00069
(0.00464) 		0.00979
(0.0375) 		3.15e-06
(8.09e-05) 		0.242
(0.418) 		0.393
(0.576)
del 18q23 137 (28%) 355 0.481
(0.642) 		0.14
(0.278) 		0.00051
(0.0035) 		0.00537
(0.0227) 		0.163
(0.313) 		1
(1.00) 		0.00263
(0.013) 		0.00154
(0.00875) 		6.47e-07
(2.14e-05) 		0.0306
(0.0892) 		0.445
(0.618)
del 21q22 2 52 (11%) 440 0.287
(0.466) 		0.216
(0.386) 		0.00181
(0.00965) 		0.0655
(0.158) 		0.0691
(0.165) 		0.176
(0.333) 		0.754
(0.874) 		0.0373
(0.104) 		0.0367
(0.102) 		0.549
(0.696) 		0.0763
(0.174)
amp 13q12 11 25 (5%) 467 0.773
(0.887) 		0.000419
(0.00319) 		0.00414
(0.0185) 		0.151
(0.292) 		0.339
(0.527) 		0.0291
(0.0867) 		0.2
(0.367) 		0.0883
(0.192) 		0.0112
(0.0415) 		0.47
(0.64) 		0.304
(0.481)
amp 18q21 31 13 (3%) 479 0.0702
(0.166) 		0.00215
(0.0111) 		0.00528
(0.0224) 		0.269
(0.452) 		0.663
(0.792) 		0.0491
(0.128) 		0.125
(0.256) 		0.361
(0.553) 		0.00501
(0.0217) 		0.392
(0.575) 		1
(1.00)
amp xq21 31 13 (3%) 479 0.62
(0.751) 		0.0336
(0.0965) 		0.0714
(0.167) 		0.467
(0.638) 		1
(1.00) 		0.316
(0.497) 		0.0813
(0.181) 		0.756
(0.874) 		0.0035
(0.0163) 		0.0697
(0.165) 		0.262
(0.441)
del 1p31 3 60 (12%) 432 0.459
(0.632) 		0.214
(0.384) 		0.00987
(0.0376) 		0.133
(0.266) 		0.0505
(0.13) 		0.236
(0.414) 		0.0491
(0.128) 		0.0618
(0.151) 		0.00012
(0.00126) 		0.292
(0.47) 		0.197
(0.363)
del 1q42 3 47 (10%) 445 0.000142
(0.00139) 		0.116
(0.242) 		0.373
(0.559) 		0.306
(0.484) 		1
(1.00) 		1
(1.00) 		0.0162
(0.0557) 		0.148
(0.29) 		0.0713
(0.167) 		0.0864
(0.189) 		0.557
(0.702)
del 2p21 46 (9%) 446 0.996
(1.00) 		0.135
(0.269) 		0.00041
(0.00316) 		0.0612
(0.15) 		0.473
(0.64) 		0.382
(0.567) 		0.0363
(0.102) 		0.0315
(0.0912) 		0.00178
(0.00965) 		0.253
(0.432) 		1
(1.00)
del 5q13 2 99 (20%) 393 0.474
(0.64) 		0.371
(0.558) 		1e-05
(0.000147) 		0.0221
(0.0711) 		0.0555
(0.139) 		0.746
(0.866) 		0.193
(0.359) 		0.00158
(0.00885) 		5.97e-09
(3.45e-07) 		0.293
(0.47) 		0.294
(0.47)
del 6p25 1 46 (9%) 446 0.157
(0.304) 		0.323
(0.506) 		0.00975
(0.0375) 		0.00596
(0.0249) 		0.233
(0.41) 		1
(1.00) 		0.614
(0.746) 		0.0018
(0.00965) 		9.13e-06
(0.000147) 		0.472
(0.64) 		0.00677
(0.0274)
del 9p23 45 (9%) 447 0.29
(0.469) 		0.492
(0.645) 		0.0265
(0.0819) 		0.02
(0.0653) 		0.0977
(0.211) 		1
(1.00) 		0.423
(0.597) 		0.00846
(0.0331) 		0.00427
(0.0189) 		0.256
(0.435) 		1
(1.00)
del 11q23 2 48 (10%) 444 0.364
(0.553) 		0.0717
(0.167) 		0.00308
(0.0147) 		0.672
(0.801) 		0.0832
(0.184) 		1
(1.00) 		0.0225
(0.0719) 		0.788
(0.897) 		9.21e-05
(0.000997) 		0.445
(0.618) 		0.658
(0.788)
del 19q13 2 52 (11%) 440 0.11
(0.234) 		0.0505
(0.13) 		0.00696
(0.028) 		0.241
(0.418) 		0.369
(0.556) 		1
(1.00) 		0.0435
(0.116) 		0.254
(0.433) 		0.000273
(0.00245) 		0.499
(0.652) 		1
(1.00)
amp 7p14 3 104 (21%) 388 0.479
(0.641) 		0.00972
(0.0375) 		0.0147
(0.0516) 		0.361
(0.553) 		0.488
(0.644) 		0.744
(0.866) 		0.00125
(0.0074) 		0.208
(0.376) 		0.000137
(0.00139) 		0.979
(1.00) 		1
(1.00)
amp 7q22 1 101 (21%) 391 0.478
(0.641) 		0.00742
(0.0297) 		0.055
(0.139) 		0.54
(0.69) 		0.485
(0.643) 		1
(1.00) 		0.00256
(0.0129) 		0.365
(0.553) 		0.000123
(0.00127) 		0.585
(0.721) 		1
(1.00)
amp 8p11 23 67 (14%) 425 0.194
(0.36) 		0.000498
(0.0035) 		0.00434
(0.0189) 		0.374
(0.559) 		0.417
(0.594) 		0.704
(0.833) 		0.0112
(0.0415) 		0.285
(0.466) 		1.9e-06
(5.49e-05) 		0.757
(0.874) 		1
(1.00)
amp 17p11 2 22 (4%) 470 0.594
(0.727) 		0.457
(0.631) 		0.00279
(0.0136) 		8.94e-05
(0.000984) 		0.736
(0.864) 		0.478
(0.641) 		0.435
(0.609) 		2.43e-06
(6.74e-05) 		0.000804
(0.0052) 		0.237
(0.416) 		1
(1.00)
del 1p22 1 58 (12%) 434 0.945
(1.00) 		0.52
(0.672) 		0.00263
(0.013) 		0.127
(0.259) 		0.195
(0.361) 		0.39
(0.575) 		0.108
(0.232) 		0.0477
(0.125) 		0.000145
(0.0014) 		0.953
(1.00) 		1
(1.00)
del 4q28 2 51 (10%) 441 0.366
(0.553) 		0.00139
(0.00799) 		0.0561
(0.139) 		0.545
(0.695) 		0.118
(0.246) 		0.647
(0.777) 		0.412
(0.592) 		0.257
(0.436) 		0.000447
(0.00335) 		0.567
(0.705) 		0.297
(0.474)
del 5q21 1 109 (22%) 383 0.491
(0.644) 		0.0528
(0.135) 		0.0226
(0.0719) 		0.883
(0.984) 		0.403
(0.584) 		0.745
(0.866) 		0.489
(0.644) 		0.562
(0.704) 		0.00132
(0.00768) 		0.0765
(0.174) 		0.734
(0.863)
del 11p11 2 34 (7%) 458 0.526
(0.679) 		0.52
(0.672) 		0.0192
(0.0636) 		0.478
(0.641) 		1
(1.00) 		0.613
(0.746) 		0.0444
(0.118) 		0.342
(0.531) 		0.0127
(0.0462) 		0.582
(0.72) 		0.00371
(0.0169)
del 12q24 32 43 (9%) 449 0.885
(0.984) 		0.811
(0.915) 		0.00318
(0.0151) 		0.0289
(0.0867) 		0.465
(0.637) 		1
(1.00) 		0.39
(0.575) 		0.0163
(0.0557) 		0.0566
(0.14) 		0.959
(1.00) 		1
(1.00)
amp 4p16 3 20 (4%) 472 0.543
(0.693) 		0.0393
(0.107) 		0.00047
(0.00339) 		0.364
(0.553) 		0.49
(0.644) 		0.445
(0.618) 		0.15
(0.292) 		0.184
(0.347) 		0.00424
(0.0188) 		0.439
(0.614) 		1
(1.00)
amp xq25 19 (4%) 473 0.286
(0.466) 		0.29
(0.469) 		0.0512
(0.131) 		0.345
(0.534) 		1
(1.00) 		1
(1.00) 		0.189
(0.355) 		0.416
(0.594) 		0.00516
(0.0222) 		0.143
(0.282) 		0.0178
(0.0598)
del 2q22 1 92 (19%) 400 0.499
(0.652) 		1.94e-05
(0.000277) 		0.135
(0.269) 		1
(1.00) 		0.858
(0.963) 		0.484
(0.643) 		0.282
(0.464) 		0.795
(0.901) 		0.0098
(0.0375) 		0.408
(0.589) 		0.415
(0.594)
del 2q22 3 85 (17%) 407 0.404
(0.584) 		0.00296
(0.0143) 		0.488
(0.644) 		0.622
(0.752) 		0.716
(0.845) 		0.481
(0.642) 		0.483
(0.643) 		0.382
(0.567) 		0.0726
(0.167) 		0.241
(0.418) 		1
(1.00)
del 3p13 78 (16%) 414 0.616
(0.747) 		0.0501
(0.13) 		0.931
(1.00) 		0.304
(0.481) 		0.0814
(0.181) 		0.253
(0.432) 		0.285
(0.466) 		0.245
(0.421) 		0.215
(0.385) 		0.774
(0.887) 		1
(1.00)
del 21q22 3 146 (30%) 346 0.294
(0.47) 		0.239
(0.417) 		0.0561
(0.139) 		0.131
(0.265) 		0.289
(0.469) 		0.568
(0.706) 		0.894
(0.992) 		0.0367
(0.102) 		0.221
(0.394) 		0.539
(0.69) 		0.133
(0.266)
del 3q29 32 (7%) 460 0.45
(0.623) 		0.645
(0.776) 		0.197
(0.363) 		0.332
(0.518) 		0.411
(0.592) 		0.229
(0.405) 		0.194
(0.36) 		0.286
(0.466) 		0.113
(0.239) 		0.944
(1.00) 		1
(1.00)
del 17q21 31 96 (20%) 396 0.471
(0.64) 		0.311
(0.49) 		0.12
(0.248) 		0.874
(0.977) 		0.604
(0.738) 		0.742
(0.866) 		0.969
(1.00) 		0.827
(0.929) 		0.333
(0.519) 		0.913
(1.00) 		0.765
(0.882)
del 1q23 1 28 (6%) 464 0.353
(0.542) 		0.141
(0.28) 		0.428
(0.602) 		1
(1.00) 		0.395
(0.577) 		1
(1.00) 		0.505
(0.658) 		0.795
(0.901) 		0.998
(1.00) 		0.874
(0.977) 		1
(1.00)
'amp_1q22' versus 'YEARS_TO_BIRTH'

P value = 0.0107 (Wilcoxon-test), Q value = 0.04

Table S1.  Gene #1: 'amp_1q22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 1(1Q22) MUTATED 38 63.6 (4.4)
AMP PEAK 1(1Q22) WILD-TYPE 443 60.8 (6.9)

Figure S1.  Get High-res Image Gene #1: 'amp_1q22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1q22' versus 'PATHOLOGY_T_STAGE'

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

Table S2.  Gene #1: 'amp_1q22' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 1(1Q22) MUTATED 4 31 5
AMP PEAK 1(1Q22) WILD-TYPE 183 257 5

Figure S2.  Get High-res Image Gene #1: 'amp_1q22' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_1q22' versus 'PATHOLOGY_N_STAGE'

P value = 0.00116 (Fisher's exact test), Q value = 0.007

Table S3.  Gene #1: 'amp_1q22' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 1(1Q22) MUTATED 22 15
AMP PEAK 1(1Q22) WILD-TYPE 321 62

Figure S3.  Get High-res Image Gene #1: 'amp_1q22' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_1q22' versus 'RADIATION_THERAPY'

P value = 0.0382 (Fisher's exact test), Q value = 0.11

Table S4.  Gene #1: 'amp_1q22' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
AMP PEAK 1(1Q22) MUTATED 27 9
AMP PEAK 1(1Q22) WILD-TYPE 363 50

Figure S4.  Get High-res Image Gene #1: 'amp_1q22' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_1q22' versus 'HISTOLOGICAL_TYPE'

P value = 0.0207 (Fisher's exact test), Q value = 0.067

Table S5.  Gene #1: 'amp_1q22' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients PROSTATE ADENOCARCINOMA ACINAR TYPE PROSTATE ADENOCARCINOMA, OTHER SUBTYPE
ALL 478 14
AMP PEAK 1(1Q22) MUTATED 36 4
AMP PEAK 1(1Q22) WILD-TYPE 442 10

Figure S5.  Get High-res Image Gene #1: 'amp_1q22' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_1q22' versus 'RESIDUAL_TUMOR'

P value = 0.0334 (Fisher's exact test), Q value = 0.096

Table S6.  Gene #1: 'amp_1q22' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 1(1Q22) MUTATED 19 20 0 0
AMP PEAK 1(1Q22) WILD-TYPE 294 124 5 15

Figure S6.  Get High-res Image Gene #1: 'amp_1q22' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_1q22' versus 'NUMBER_OF_LYMPH_NODES'

P value = 6.66e-05 (Wilcoxon-test), Q value = 8e-04

Table S7.  Gene #1: 'amp_1q22' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 1(1Q22) MUTATED 37 1.2 (2.7)
AMP PEAK 1(1Q22) WILD-TYPE 365 0.4 (1.1)

Figure S7.  Get High-res Image Gene #1: 'amp_1q22' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_1q22' versus 'GLEASON_SCORE'

P value = 1.53e-07 (Wilcoxon-test), Q value = 5.6e-06

Table S8.  Gene #1: 'amp_1q22' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 1(1Q22) MUTATED 40 8.4 (0.9)
AMP PEAK 1(1Q22) WILD-TYPE 452 7.5 (1.0)

Figure S8.  Get High-res Image Gene #1: 'amp_1q22' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_3q21.3' versus 'YEARS_TO_BIRTH'

P value = 0.00251 (Wilcoxon-test), Q value = 0.013

Table S9.  Gene #2: 'amp_3q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 2(3Q21.3) MUTATED 72 63.2 (6.9)
AMP PEAK 2(3Q21.3) WILD-TYPE 409 60.6 (6.7)

Figure S9.  Get High-res Image Gene #2: 'amp_3q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3q21.3' versus 'PATHOLOGY_T_STAGE'

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

Table S10.  Gene #2: 'amp_3q21.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 2(3Q21.3) MUTATED 12 57 5
AMP PEAK 2(3Q21.3) WILD-TYPE 175 231 5

Figure S10.  Get High-res Image Gene #2: 'amp_3q21.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_3q21.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00207 (Fisher's exact test), Q value = 0.011

Table S11.  Gene #2: 'amp_3q21.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 2(3Q21.3) MUTATED 48 23
AMP PEAK 2(3Q21.3) WILD-TYPE 295 54

Figure S11.  Get High-res Image Gene #2: 'amp_3q21.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_3q21.3' versus 'RADIATION_THERAPY'

P value = 0.0431 (Fisher's exact test), Q value = 0.12

Table S12.  Gene #2: 'amp_3q21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
AMP PEAK 2(3Q21.3) MUTATED 50 14
AMP PEAK 2(3Q21.3) WILD-TYPE 340 45

Figure S12.  Get High-res Image Gene #2: 'amp_3q21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_3q21.3' versus 'RESIDUAL_TUMOR'

P value = 5e-04 (Fisher's exact test), Q value = 0.0035

Table S13.  Gene #2: 'amp_3q21.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 2(3Q21.3) MUTATED 32 32 2 5
AMP PEAK 2(3Q21.3) WILD-TYPE 281 112 3 10

Figure S13.  Get High-res Image Gene #2: 'amp_3q21.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_3q21.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 5.13e-05 (Wilcoxon-test), Q value = 0.00065

Table S14.  Gene #2: 'amp_3q21.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 2(3Q21.3) MUTATED 66 1.0 (1.9)
AMP PEAK 2(3Q21.3) WILD-TYPE 336 0.3 (1.2)

Figure S14.  Get High-res Image Gene #2: 'amp_3q21.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_3q21.3' versus 'GLEASON_SCORE'

P value = 3.56e-11 (Wilcoxon-test), Q value = 6.2e-09

Table S15.  Gene #2: 'amp_3q21.3' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 2(3Q21.3) MUTATED 75 8.3 (0.9)
AMP PEAK 2(3Q21.3) WILD-TYPE 417 7.5 (1.0)

Figure S15.  Get High-res Image Gene #2: 'amp_3q21.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_3q26.2' versus 'YEARS_TO_BIRTH'

P value = 0.0225 (Wilcoxon-test), Q value = 0.072

Table S16.  Gene #3: 'amp_3q26.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 3(3Q26.2) MUTATED 83 62.6 (6.8)
AMP PEAK 3(3Q26.2) WILD-TYPE 398 60.6 (6.8)

Figure S16.  Get High-res Image Gene #3: 'amp_3q26.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3q26.2' versus 'PATHOLOGY_T_STAGE'

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

Table S17.  Gene #3: 'amp_3q26.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 3(3Q26.2) MUTATED 16 63 6
AMP PEAK 3(3Q26.2) WILD-TYPE 171 225 4

Figure S17.  Get High-res Image Gene #3: 'amp_3q26.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_3q26.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.000717 (Fisher's exact test), Q value = 0.0047

Table S18.  Gene #3: 'amp_3q26.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 3(3Q26.2) MUTATED 55 26
AMP PEAK 3(3Q26.2) WILD-TYPE 288 51

Figure S18.  Get High-res Image Gene #3: 'amp_3q26.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_3q26.2' versus 'RESIDUAL_TUMOR'

P value = 0.00014 (Fisher's exact test), Q value = 0.0014

Table S19.  Gene #3: 'amp_3q26.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 3(3Q26.2) MUTATED 37 39 2 4
AMP PEAK 3(3Q26.2) WILD-TYPE 276 105 3 11

Figure S19.  Get High-res Image Gene #3: 'amp_3q26.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_3q26.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 2.93e-05 (Wilcoxon-test), Q value = 4e-04

Table S20.  Gene #3: 'amp_3q26.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 3(3Q26.2) MUTATED 77 1.0 (1.9)
AMP PEAK 3(3Q26.2) WILD-TYPE 325 0.3 (1.2)

Figure S20.  Get High-res Image Gene #3: 'amp_3q26.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_3q26.2' versus 'GLEASON_SCORE'

P value = 1.18e-09 (Wilcoxon-test), Q value = 1e-07

Table S21.  Gene #3: 'amp_3q26.2' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 3(3Q26.2) MUTATED 86 8.2 (1.0)
AMP PEAK 3(3Q26.2) WILD-TYPE 406 7.5 (1.0)

Figure S21.  Get High-res Image Gene #3: 'amp_3q26.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_3q26.2' versus 'PSA_VALUE'

P value = 0.0539 (Wilcoxon-test), Q value = 0.14

Table S22.  Gene #3: 'amp_3q26.2' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
AMP PEAK 3(3Q26.2) MUTATED 75 2.7 (8.0)
AMP PEAK 3(3Q26.2) WILD-TYPE 360 1.6 (17.2)

Figure S22.  Get High-res Image Gene #3: 'amp_3q26.2' versus Clinical Feature #10: 'PSA_VALUE'

'amp_4p16.3' versus 'YEARS_TO_BIRTH'

P value = 0.0393 (Wilcoxon-test), Q value = 0.11

Table S23.  Gene #4: 'amp_4p16.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 4(4P16.3) MUTATED 19 63.7 (6.4)
AMP PEAK 4(4P16.3) WILD-TYPE 462 60.9 (6.8)

Figure S23.  Get High-res Image Gene #4: 'amp_4p16.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_4p16.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00047 (Fisher's exact test), Q value = 0.0034

Table S24.  Gene #4: 'amp_4p16.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 4(4P16.3) MUTATED 1 17 2
AMP PEAK 4(4P16.3) WILD-TYPE 186 271 8

Figure S24.  Get High-res Image Gene #4: 'amp_4p16.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_4p16.3' versus 'GLEASON_SCORE'

P value = 0.00424 (Wilcoxon-test), Q value = 0.019

Table S25.  Gene #4: 'amp_4p16.3' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 4(4P16.3) MUTATED 20 8.2 (1.0)
AMP PEAK 4(4P16.3) WILD-TYPE 472 7.6 (1.0)

Figure S25.  Get High-res Image Gene #4: 'amp_4p16.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_4q13.3' versus 'YEARS_TO_BIRTH'

P value = 0.0193 (Wilcoxon-test), Q value = 0.064

Table S26.  Gene #5: 'amp_4q13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 5(4Q13.3) MUTATED 20 64.6 (5.5)
AMP PEAK 5(4Q13.3) WILD-TYPE 461 60.8 (6.8)

Figure S26.  Get High-res Image Gene #5: 'amp_4q13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_4q13.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00193 (Fisher's exact test), Q value = 0.01

Table S27.  Gene #5: 'amp_4q13.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 5(4Q13.3) MUTATED 2 18 2
AMP PEAK 5(4Q13.3) WILD-TYPE 185 270 8

Figure S27.  Get High-res Image Gene #5: 'amp_4q13.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_4q13.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00051 (Fisher's exact test), Q value = 0.0035

Table S28.  Gene #5: 'amp_4q13.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 5(4Q13.3) MUTATED 11 11
AMP PEAK 5(4Q13.3) WILD-TYPE 332 66

Figure S28.  Get High-res Image Gene #5: 'amp_4q13.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_4q13.3' versus 'RESIDUAL_TUMOR'

P value = 0.00526 (Fisher's exact test), Q value = 0.022

Table S29.  Gene #5: 'amp_4q13.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 5(4Q13.3) MUTATED 7 14 0 1
AMP PEAK 5(4Q13.3) WILD-TYPE 306 130 5 14

Figure S29.  Get High-res Image Gene #5: 'amp_4q13.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_4q13.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 5.9e-05 (Wilcoxon-test), Q value = 0.00072

Table S30.  Gene #5: 'amp_4q13.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 5(4Q13.3) MUTATED 21 1.2 (1.7)
AMP PEAK 5(4Q13.3) WILD-TYPE 381 0.4 (1.3)

Figure S30.  Get High-res Image Gene #5: 'amp_4q13.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_4q13.3' versus 'GLEASON_SCORE'

P value = 0.000271 (Wilcoxon-test), Q value = 0.0025

Table S31.  Gene #5: 'amp_4q13.3' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 5(4Q13.3) MUTATED 22 8.4 (1.0)
AMP PEAK 5(4Q13.3) WILD-TYPE 470 7.6 (1.0)

Figure S31.  Get High-res Image Gene #5: 'amp_4q13.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_5q35.3' versus 'YEARS_TO_BIRTH'

P value = 2.58e-07 (Wilcoxon-test), Q value = 8.9e-06

Table S32.  Gene #6: 'amp_5q35.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 6(5Q35.3) MUTATED 28 67.1 (4.0)
AMP PEAK 6(5Q35.3) WILD-TYPE 453 60.6 (6.8)

Figure S32.  Get High-res Image Gene #6: 'amp_5q35.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_5q35.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00022 (Fisher's exact test), Q value = 0.0021

Table S33.  Gene #6: 'amp_5q35.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 6(5Q35.3) MUTATED 2 24 2
AMP PEAK 6(5Q35.3) WILD-TYPE 185 264 8

Figure S33.  Get High-res Image Gene #6: 'amp_5q35.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_5q35.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.000701 (Fisher's exact test), Q value = 0.0047

Table S34.  Gene #6: 'amp_5q35.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 6(5Q35.3) MUTATED 14 12
AMP PEAK 6(5Q35.3) WILD-TYPE 329 65

Figure S34.  Get High-res Image Gene #6: 'amp_5q35.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_5q35.3' versus 'RESIDUAL_TUMOR'

P value = 0.0658 (Fisher's exact test), Q value = 0.16

Table S35.  Gene #6: 'amp_5q35.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 6(5Q35.3) MUTATED 13 13 1 1
AMP PEAK 6(5Q35.3) WILD-TYPE 300 131 4 14

Figure S35.  Get High-res Image Gene #6: 'amp_5q35.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_5q35.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 7.33e-05 (Wilcoxon-test), Q value = 0.00086

Table S36.  Gene #6: 'amp_5q35.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 6(5Q35.3) MUTATED 25 1.8 (3.5)
AMP PEAK 6(5Q35.3) WILD-TYPE 377 0.3 (1.0)

Figure S36.  Get High-res Image Gene #6: 'amp_5q35.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_5q35.3' versus 'GLEASON_SCORE'

P value = 3.95e-05 (Wilcoxon-test), Q value = 0.00052

Table S37.  Gene #6: 'amp_5q35.3' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 6(5Q35.3) MUTATED 28 8.4 (0.8)
AMP PEAK 6(5Q35.3) WILD-TYPE 464 7.6 (1.0)

Figure S37.  Get High-res Image Gene #6: 'amp_5q35.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_7p14.3' versus 'YEARS_TO_BIRTH'

P value = 0.00972 (Wilcoxon-test), Q value = 0.038

Table S38.  Gene #7: 'amp_7p14.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 7(7P14.3) MUTATED 101 62.4 (6.7)
AMP PEAK 7(7P14.3) WILD-TYPE 380 60.6 (6.8)

Figure S38.  Get High-res Image Gene #7: 'amp_7p14.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7p14.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0147 (Fisher's exact test), Q value = 0.052

Table S39.  Gene #7: 'amp_7p14.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 7(7P14.3) MUTATED 28 74 2
AMP PEAK 7(7P14.3) WILD-TYPE 159 214 8

Figure S39.  Get High-res Image Gene #7: 'amp_7p14.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_7p14.3' versus 'RESIDUAL_TUMOR'

P value = 0.00125 (Fisher's exact test), Q value = 0.0074

Table S40.  Gene #7: 'amp_7p14.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 7(7P14.3) MUTATED 50 46 1 4
AMP PEAK 7(7P14.3) WILD-TYPE 263 98 4 11

Figure S40.  Get High-res Image Gene #7: 'amp_7p14.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_7p14.3' versus 'GLEASON_SCORE'

P value = 0.000137 (Wilcoxon-test), Q value = 0.0014

Table S41.  Gene #7: 'amp_7p14.3' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 7(7P14.3) MUTATED 104 8.0 (1.1)
AMP PEAK 7(7P14.3) WILD-TYPE 388 7.5 (1.0)

Figure S41.  Get High-res Image Gene #7: 'amp_7p14.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_7q22.1' versus 'YEARS_TO_BIRTH'

P value = 0.00742 (Wilcoxon-test), Q value = 0.03

Table S42.  Gene #8: 'amp_7q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 8(7Q22.1) MUTATED 99 62.5 (6.8)
AMP PEAK 8(7Q22.1) WILD-TYPE 382 60.6 (6.8)

Figure S42.  Get High-res Image Gene #8: 'amp_7q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q22.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.055 (Fisher's exact test), Q value = 0.14

Table S43.  Gene #8: 'amp_7q22.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 8(7Q22.1) MUTATED 29 70 2
AMP PEAK 8(7Q22.1) WILD-TYPE 158 218 8

Figure S43.  Get High-res Image Gene #8: 'amp_7q22.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_7q22.1' versus 'RESIDUAL_TUMOR'

P value = 0.00256 (Fisher's exact test), Q value = 0.013

Table S44.  Gene #8: 'amp_7q22.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 8(7Q22.1) MUTATED 50 45 1 3
AMP PEAK 8(7Q22.1) WILD-TYPE 263 99 4 12

Figure S44.  Get High-res Image Gene #8: 'amp_7q22.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_7q22.1' versus 'GLEASON_SCORE'

P value = 0.000123 (Wilcoxon-test), Q value = 0.0013

Table S45.  Gene #8: 'amp_7q22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 8(7Q22.1) MUTATED 101 8.0 (1.1)
AMP PEAK 8(7Q22.1) WILD-TYPE 391 7.5 (1.0)

Figure S45.  Get High-res Image Gene #8: 'amp_7q22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_8p11.23' versus 'YEARS_TO_BIRTH'

P value = 0.000498 (Wilcoxon-test), Q value = 0.0035

Table S46.  Gene #9: 'amp_8p11.23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 9(8P11.23) MUTATED 64 63.7 (6.5)
AMP PEAK 9(8P11.23) WILD-TYPE 417 60.6 (6.8)

Figure S46.  Get High-res Image Gene #9: 'amp_8p11.23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8p11.23' versus 'PATHOLOGY_T_STAGE'

P value = 0.00434 (Fisher's exact test), Q value = 0.019

Table S47.  Gene #9: 'amp_8p11.23' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 9(8P11.23) MUTATED 15 49 3
AMP PEAK 9(8P11.23) WILD-TYPE 172 239 7

Figure S47.  Get High-res Image Gene #9: 'amp_8p11.23' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_8p11.23' versus 'RESIDUAL_TUMOR'

P value = 0.0112 (Fisher's exact test), Q value = 0.042

Table S48.  Gene #9: 'amp_8p11.23' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 9(8P11.23) MUTATED 31 29 1 3
AMP PEAK 9(8P11.23) WILD-TYPE 282 115 4 12

Figure S48.  Get High-res Image Gene #9: 'amp_8p11.23' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_8p11.23' versus 'GLEASON_SCORE'

P value = 1.9e-06 (Wilcoxon-test), Q value = 5.5e-05

Table S49.  Gene #9: 'amp_8p11.23' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 9(8P11.23) MUTATED 67 8.2 (1.0)
AMP PEAK 9(8P11.23) WILD-TYPE 425 7.5 (1.0)

Figure S49.  Get High-res Image Gene #9: 'amp_8p11.23' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_8q22.1' versus 'YEARS_TO_BIRTH'

P value = 0.0851 (Wilcoxon-test), Q value = 0.19

Table S50.  Gene #10: 'amp_8q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 10(8Q22.1) MUTATED 154 61.7 (6.3)
AMP PEAK 10(8Q22.1) WILD-TYPE 327 60.6 (7.0)

Figure S50.  Get High-res Image Gene #10: 'amp_8q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q22.1' versus 'PATHOLOGY_T_STAGE'

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

Table S51.  Gene #10: 'amp_8q22.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 10(8Q22.1) MUTATED 33 117 6
AMP PEAK 10(8Q22.1) WILD-TYPE 154 171 4

Figure S51.  Get High-res Image Gene #10: 'amp_8q22.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_8q22.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00215 (Fisher's exact test), Q value = 0.011

Table S52.  Gene #10: 'amp_8q22.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 10(8Q22.1) MUTATED 107 39
AMP PEAK 10(8Q22.1) WILD-TYPE 236 38

Figure S52.  Get High-res Image Gene #10: 'amp_8q22.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_8q22.1' versus 'RADIATION_THERAPY'

P value = 0.0151 (Fisher's exact test), Q value = 0.053

Table S53.  Gene #10: 'amp_8q22.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
AMP PEAK 10(8Q22.1) MUTATED 113 27
AMP PEAK 10(8Q22.1) WILD-TYPE 277 32

Figure S53.  Get High-res Image Gene #10: 'amp_8q22.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_8q22.1' versus 'RESIDUAL_TUMOR'

P value = 3e-05 (Fisher's exact test), Q value = 4e-04

Table S54.  Gene #10: 'amp_8q22.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 10(8Q22.1) MUTATED 77 67 1 7
AMP PEAK 10(8Q22.1) WILD-TYPE 236 77 4 8

Figure S54.  Get High-res Image Gene #10: 'amp_8q22.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_8q22.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000321 (Wilcoxon-test), Q value = 0.0027

Table S55.  Gene #10: 'amp_8q22.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 10(8Q22.1) MUTATED 139 0.7 (1.6)
AMP PEAK 10(8Q22.1) WILD-TYPE 263 0.3 (1.2)

Figure S55.  Get High-res Image Gene #10: 'amp_8q22.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_8q22.1' versus 'GLEASON_SCORE'

P value = 1.45e-13 (Wilcoxon-test), Q value = 1e-10

Table S56.  Gene #10: 'amp_8q22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 10(8Q22.1) MUTATED 157 8.1 (1.0)
AMP PEAK 10(8Q22.1) WILD-TYPE 335 7.4 (0.9)

Figure S56.  Get High-res Image Gene #10: 'amp_8q22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_8q22.1' versus 'PSA_VALUE'

P value = 0.0555 (Wilcoxon-test), Q value = 0.14

Table S57.  Gene #10: 'amp_8q22.1' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
AMP PEAK 10(8Q22.1) MUTATED 138 3.7 (27.8)
AMP PEAK 10(8Q22.1) WILD-TYPE 297 0.8 (3.6)

Figure S57.  Get High-res Image Gene #10: 'amp_8q22.1' versus Clinical Feature #10: 'PSA_VALUE'

'amp_8q24.21' versus 'YEARS_TO_BIRTH'

P value = 0.053 (Wilcoxon-test), Q value = 0.14

Table S58.  Gene #11: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 11(8Q24.21) MUTATED 148 61.9 (6.3)
AMP PEAK 11(8Q24.21) WILD-TYPE 333 60.6 (7.0)

Figure S58.  Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.21' versus 'PATHOLOGY_T_STAGE'

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

Table S59.  Gene #11: 'amp_8q24.21' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 11(8Q24.21) MUTATED 33 112 6
AMP PEAK 11(8Q24.21) WILD-TYPE 154 176 4

Figure S59.  Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_8q24.21' versus 'PATHOLOGY_N_STAGE'

P value = 0.000759 (Fisher's exact test), Q value = 0.005

Table S60.  Gene #11: 'amp_8q24.21' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 11(8Q24.21) MUTATED 102 39
AMP PEAK 11(8Q24.21) WILD-TYPE 241 38

Figure S60.  Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_8q24.21' versus 'RADIATION_THERAPY'

P value = 0.0468 (Fisher's exact test), Q value = 0.12

Table S61.  Gene #11: 'amp_8q24.21' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
AMP PEAK 11(8Q24.21) MUTATED 108 24
AMP PEAK 11(8Q24.21) WILD-TYPE 282 35

Figure S61.  Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_8q24.21' versus 'RESIDUAL_TUMOR'

P value = 0.00014 (Fisher's exact test), Q value = 0.0014

Table S62.  Gene #11: 'amp_8q24.21' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 11(8Q24.21) MUTATED 76 63 1 7
AMP PEAK 11(8Q24.21) WILD-TYPE 237 81 4 8

Figure S62.  Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_8q24.21' versus 'NUMBER_OF_LYMPH_NODES'

P value = 9.4e-05 (Wilcoxon-test), Q value = 0.001

Table S63.  Gene #11: 'amp_8q24.21' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 11(8Q24.21) MUTATED 134 0.7 (1.4)
AMP PEAK 11(8Q24.21) WILD-TYPE 268 0.3 (1.3)

Figure S63.  Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_8q24.21' versus 'GLEASON_SCORE'

P value = 9.12e-13 (Wilcoxon-test), Q value = 2.1e-10

Table S64.  Gene #11: 'amp_8q24.21' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 11(8Q24.21) MUTATED 152 8.1 (1.0)
AMP PEAK 11(8Q24.21) WILD-TYPE 340 7.4 (0.9)

Figure S64.  Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_8q24.21' versus 'PSA_VALUE'

P value = 0.0294 (Wilcoxon-test), Q value = 0.087

Table S65.  Gene #11: 'amp_8q24.21' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
AMP PEAK 11(8Q24.21) MUTATED 131 4.0 (28.5)
AMP PEAK 11(8Q24.21) WILD-TYPE 304 0.8 (3.5)

Figure S65.  Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #10: 'PSA_VALUE'

'amp_9q33.3' versus 'YEARS_TO_BIRTH'

P value = 0.0246 (Wilcoxon-test), Q value = 0.078

Table S66.  Gene #12: 'amp_9q33.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 12(9Q33.3) MUTATED 60 62.9 (6.3)
AMP PEAK 12(9Q33.3) WILD-TYPE 421 60.7 (6.8)

Figure S66.  Get High-res Image Gene #12: 'amp_9q33.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_9q33.3' versus 'PATHOLOGY_T_STAGE'

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

Table S67.  Gene #12: 'amp_9q33.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 12(9Q33.3) MUTATED 5 53 3
AMP PEAK 12(9Q33.3) WILD-TYPE 182 235 7

Figure S67.  Get High-res Image Gene #12: 'amp_9q33.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_9q33.3' versus 'PATHOLOGY_N_STAGE'

P value = 1.87e-08 (Fisher's exact test), Q value = 8.6e-07

Table S68.  Gene #12: 'amp_9q33.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 12(9Q33.3) MUTATED 31 28
AMP PEAK 12(9Q33.3) WILD-TYPE 312 49

Figure S68.  Get High-res Image Gene #12: 'amp_9q33.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_9q33.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0865 (Fisher's exact test), Q value = 0.19

Table S69.  Gene #12: 'amp_9q33.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients PROSTATE ADENOCARCINOMA ACINAR TYPE PROSTATE ADENOCARCINOMA, OTHER SUBTYPE
ALL 478 14
AMP PEAK 12(9Q33.3) MUTATED 58 4
AMP PEAK 12(9Q33.3) WILD-TYPE 420 10

Figure S69.  Get High-res Image Gene #12: 'amp_9q33.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_9q33.3' versus 'RESIDUAL_TUMOR'

P value = 0.00038 (Fisher's exact test), Q value = 0.003

Table S70.  Gene #12: 'amp_9q33.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 12(9Q33.3) MUTATED 26 32 1 1
AMP PEAK 12(9Q33.3) WILD-TYPE 287 112 4 14

Figure S70.  Get High-res Image Gene #12: 'amp_9q33.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_9q33.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 9.81e-11 (Wilcoxon-test), Q value = 1.4e-08

Table S71.  Gene #12: 'amp_9q33.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 12(9Q33.3) MUTATED 59 1.3 (2.5)
AMP PEAK 12(9Q33.3) WILD-TYPE 343 0.3 (1.0)

Figure S71.  Get High-res Image Gene #12: 'amp_9q33.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_9q33.3' versus 'GLEASON_SCORE'

P value = 6.13e-13 (Wilcoxon-test), Q value = 2.1e-10

Table S72.  Gene #12: 'amp_9q33.3' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 12(9Q33.3) MUTATED 62 8.5 (0.8)
AMP PEAK 12(9Q33.3) WILD-TYPE 430 7.5 (1.0)

Figure S72.  Get High-res Image Gene #12: 'amp_9q33.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_11q13.2' versus 'YEARS_TO_BIRTH'

P value = 5e-04 (Wilcoxon-test), Q value = 0.0035

Table S73.  Gene #13: 'amp_11q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 13(11Q13.2) MUTATED 46 64.1 (5.8)
AMP PEAK 13(11Q13.2) WILD-TYPE 435 60.7 (6.8)

Figure S73.  Get High-res Image Gene #13: 'amp_11q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_11q13.2' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S74.  Gene #13: 'amp_11q13.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 13(11Q13.2) MUTATED 5 40 3
AMP PEAK 13(11Q13.2) WILD-TYPE 182 248 7

Figure S74.  Get High-res Image Gene #13: 'amp_11q13.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_11q13.2' versus 'PATHOLOGY_N_STAGE'

P value = 9.47e-06 (Fisher's exact test), Q value = 0.00015

Table S75.  Gene #13: 'amp_11q13.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 13(11Q13.2) MUTATED 24 20
AMP PEAK 13(11Q13.2) WILD-TYPE 319 57

Figure S75.  Get High-res Image Gene #13: 'amp_11q13.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_11q13.2' versus 'RESIDUAL_TUMOR'

P value = 0.00161 (Fisher's exact test), Q value = 0.0089

Table S76.  Gene #13: 'amp_11q13.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 13(11Q13.2) MUTATED 20 26 0 2
AMP PEAK 13(11Q13.2) WILD-TYPE 293 118 5 13

Figure S76.  Get High-res Image Gene #13: 'amp_11q13.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_11q13.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 9.95e-08 (Wilcoxon-test), Q value = 3.8e-06

Table S77.  Gene #13: 'amp_11q13.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 13(11Q13.2) MUTATED 42 1.4 (2.8)
AMP PEAK 13(11Q13.2) WILD-TYPE 360 0.3 (1.0)

Figure S77.  Get High-res Image Gene #13: 'amp_11q13.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_11q13.2' versus 'GLEASON_SCORE'

P value = 1.09e-08 (Wilcoxon-test), Q value = 5.4e-07

Table S78.  Gene #13: 'amp_11q13.2' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 13(11Q13.2) MUTATED 48 8.4 (0.9)
AMP PEAK 13(11Q13.2) WILD-TYPE 444 7.5 (1.0)

Figure S78.  Get High-res Image Gene #13: 'amp_11q13.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_12q23.1' versus 'YEARS_TO_BIRTH'

P value = 0.077 (Wilcoxon-test), Q value = 0.17

Table S79.  Gene #14: 'amp_12q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 14(12Q23.1) MUTATED 34 63.1 (6.4)
AMP PEAK 14(12Q23.1) WILD-TYPE 447 60.8 (6.8)

Figure S79.  Get High-res Image Gene #14: 'amp_12q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12q23.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00032 (Fisher's exact test), Q value = 0.0027

Table S80.  Gene #14: 'amp_12q23.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 14(12Q23.1) MUTATED 4 30 2
AMP PEAK 14(12Q23.1) WILD-TYPE 183 258 8

Figure S80.  Get High-res Image Gene #14: 'amp_12q23.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_12q23.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00127 (Fisher's exact test), Q value = 0.0075

Table S81.  Gene #14: 'amp_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 14(12Q23.1) MUTATED 18 13
AMP PEAK 14(12Q23.1) WILD-TYPE 325 64

Figure S81.  Get High-res Image Gene #14: 'amp_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_12q23.1' versus 'RADIATION_THERAPY'

P value = 0.0433 (Fisher's exact test), Q value = 0.12

Table S82.  Gene #14: 'amp_12q23.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
AMP PEAK 14(12Q23.1) MUTATED 22 8
AMP PEAK 14(12Q23.1) WILD-TYPE 368 51

Figure S82.  Get High-res Image Gene #14: 'amp_12q23.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_12q23.1' versus 'RESIDUAL_TUMOR'

P value = 0.00029 (Fisher's exact test), Q value = 0.0025

Table S83.  Gene #14: 'amp_12q23.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 14(12Q23.1) MUTATED 13 22 1 0
AMP PEAK 14(12Q23.1) WILD-TYPE 300 122 4 15

Figure S83.  Get High-res Image Gene #14: 'amp_12q23.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_12q23.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000371 (Wilcoxon-test), Q value = 0.003

Table S84.  Gene #14: 'amp_12q23.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 14(12Q23.1) MUTATED 30 1.2 (2.4)
AMP PEAK 14(12Q23.1) WILD-TYPE 372 0.4 (1.2)

Figure S84.  Get High-res Image Gene #14: 'amp_12q23.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_12q23.1' versus 'GLEASON_SCORE'

P value = 3.01e-06 (Wilcoxon-test), Q value = 8e-05

Table S85.  Gene #14: 'amp_12q23.1' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 14(12Q23.1) MUTATED 36 8.4 (1.0)
AMP PEAK 14(12Q23.1) WILD-TYPE 456 7.5 (1.0)

Figure S85.  Get High-res Image Gene #14: 'amp_12q23.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_12q23.1' versus 'PSA_VALUE'

P value = 0.0708 (Wilcoxon-test), Q value = 0.17

Table S86.  Gene #14: 'amp_12q23.1' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
AMP PEAK 14(12Q23.1) MUTATED 29 1.1 (2.7)
AMP PEAK 14(12Q23.1) WILD-TYPE 406 1.8 (16.5)

Figure S86.  Get High-res Image Gene #14: 'amp_12q23.1' versus Clinical Feature #10: 'PSA_VALUE'

'amp_13q12.11' versus 'YEARS_TO_BIRTH'

P value = 0.000419 (Wilcoxon-test), Q value = 0.0032

Table S87.  Gene #15: 'amp_13q12.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 15(13Q12.11) MUTATED 24 65.5 (4.2)
AMP PEAK 15(13Q12.11) WILD-TYPE 457 60.7 (6.8)

Figure S87.  Get High-res Image Gene #15: 'amp_13q12.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_13q12.11' versus 'PATHOLOGY_T_STAGE'

P value = 0.00414 (Fisher's exact test), Q value = 0.019

Table S88.  Gene #15: 'amp_13q12.11' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 15(13Q12.11) MUTATED 5 17 3
AMP PEAK 15(13Q12.11) WILD-TYPE 182 271 7

Figure S88.  Get High-res Image Gene #15: 'amp_13q12.11' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_13q12.11' versus 'HISTOLOGICAL_TYPE'

P value = 0.0291 (Fisher's exact test), Q value = 0.087

Table S89.  Gene #15: 'amp_13q12.11' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients PROSTATE ADENOCARCINOMA ACINAR TYPE PROSTATE ADENOCARCINOMA, OTHER SUBTYPE
ALL 478 14
AMP PEAK 15(13Q12.11) MUTATED 22 3
AMP PEAK 15(13Q12.11) WILD-TYPE 456 11

Figure S89.  Get High-res Image Gene #15: 'amp_13q12.11' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_13q12.11' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0883 (Wilcoxon-test), Q value = 0.19

Table S90.  Gene #15: 'amp_13q12.11' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 15(13Q12.11) MUTATED 21 0.7 (1.4)
AMP PEAK 15(13Q12.11) WILD-TYPE 381 0.4 (1.4)

Figure S90.  Get High-res Image Gene #15: 'amp_13q12.11' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_13q12.11' versus 'GLEASON_SCORE'

P value = 0.0112 (Wilcoxon-test), Q value = 0.042

Table S91.  Gene #15: 'amp_13q12.11' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 15(13Q12.11) MUTATED 25 8.1 (1.1)
AMP PEAK 15(13Q12.11) WILD-TYPE 467 7.6 (1.0)

Figure S91.  Get High-res Image Gene #15: 'amp_13q12.11' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_14q21.1' versus 'YEARS_TO_BIRTH'

P value = 0.0372 (Wilcoxon-test), Q value = 0.1

Table S92.  Gene #16: 'amp_14q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 16(14Q21.1) MUTATED 28 63.4 (5.6)
AMP PEAK 16(14Q21.1) WILD-TYPE 453 60.8 (6.8)

Figure S92.  Get High-res Image Gene #16: 'amp_14q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_14q21.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0694 (Fisher's exact test), Q value = 0.17

Table S93.  Gene #16: 'amp_14q21.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 16(14Q21.1) MUTATED 6 24 0
AMP PEAK 16(14Q21.1) WILD-TYPE 181 264 10

Figure S93.  Get High-res Image Gene #16: 'amp_14q21.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_14q21.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0147 (Fisher's exact test), Q value = 0.052

Table S94.  Gene #16: 'amp_14q21.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 16(14Q21.1) MUTATED 16 10
AMP PEAK 16(14Q21.1) WILD-TYPE 327 67

Figure S94.  Get High-res Image Gene #16: 'amp_14q21.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_14q21.1' versus 'RADIATION_THERAPY'

P value = 0.00329 (Fisher's exact test), Q value = 0.016

Table S95.  Gene #16: 'amp_14q21.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
AMP PEAK 16(14Q21.1) MUTATED 17 9
AMP PEAK 16(14Q21.1) WILD-TYPE 373 50

Figure S95.  Get High-res Image Gene #16: 'amp_14q21.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_14q21.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00605 (Wilcoxon-test), Q value = 0.025

Table S96.  Gene #16: 'amp_14q21.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 16(14Q21.1) MUTATED 26 1.2 (2.0)
AMP PEAK 16(14Q21.1) WILD-TYPE 376 0.4 (1.3)

Figure S96.  Get High-res Image Gene #16: 'amp_14q21.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_14q21.1' versus 'GLEASON_SCORE'

P value = 8.39e-05 (Wilcoxon-test), Q value = 0.00094

Table S97.  Gene #16: 'amp_14q21.1' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 16(14Q21.1) MUTATED 30 8.3 (0.9)
AMP PEAK 16(14Q21.1) WILD-TYPE 462 7.6 (1.0)

Figure S97.  Get High-res Image Gene #16: 'amp_14q21.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_15q11.2' versus 'Time to Death'

P value = 0.0849 (logrank test), Q value = 0.19

Table S98.  Gene #17: 'amp_15q11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 492 9 0.8 - 165.2 (30.6)
AMP PEAK 17(15Q11.2) MUTATED 16 1 4.3 - 69.3 (29.8)
AMP PEAK 17(15Q11.2) WILD-TYPE 476 8 0.8 - 165.2 (30.6)

Figure S98.  Get High-res Image Gene #17: 'amp_15q11.2' versus Clinical Feature #1: 'Time to Death'

'amp_15q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.0738 (Wilcoxon-test), Q value = 0.17

Table S99.  Gene #17: 'amp_15q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 17(15Q11.2) MUTATED 15 63.8 (7.4)
AMP PEAK 17(15Q11.2) WILD-TYPE 466 60.9 (6.8)

Figure S99.  Get High-res Image Gene #17: 'amp_15q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_15q11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.109 (Fisher's exact test), Q value = 0.23

Table S100.  Gene #17: 'amp_15q11.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 17(15Q11.2) MUTATED 3 12 1
AMP PEAK 17(15Q11.2) WILD-TYPE 184 276 9

Figure S100.  Get High-res Image Gene #17: 'amp_15q11.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_15q11.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.000298 (Fisher's exact test), Q value = 0.0026

Table S101.  Gene #17: 'amp_15q11.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 17(15Q11.2) MUTATED 6 9
AMP PEAK 17(15Q11.2) WILD-TYPE 337 68

Figure S101.  Get High-res Image Gene #17: 'amp_15q11.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_15q11.2' versus 'RADIATION_THERAPY'

P value = 0.0772 (Fisher's exact test), Q value = 0.17

Table S102.  Gene #17: 'amp_15q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
AMP PEAK 17(15Q11.2) MUTATED 9 4
AMP PEAK 17(15Q11.2) WILD-TYPE 381 55

Figure S102.  Get High-res Image Gene #17: 'amp_15q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_15q11.2' versus 'RESIDUAL_TUMOR'

P value = 0.0142 (Fisher's exact test), Q value = 0.05

Table S103.  Gene #17: 'amp_15q11.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 17(15Q11.2) MUTATED 5 11 0 0
AMP PEAK 17(15Q11.2) WILD-TYPE 308 133 5 15

Figure S103.  Get High-res Image Gene #17: 'amp_15q11.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_15q11.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 9.6e-07 (Wilcoxon-test), Q value = 3e-05

Table S104.  Gene #17: 'amp_15q11.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 17(15Q11.2) MUTATED 15 1.3 (1.2)
AMP PEAK 17(15Q11.2) WILD-TYPE 387 0.4 (1.4)

Figure S104.  Get High-res Image Gene #17: 'amp_15q11.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_15q11.2' versus 'GLEASON_SCORE'

P value = 0.00139 (Wilcoxon-test), Q value = 0.008

Table S105.  Gene #17: 'amp_15q11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 17(15Q11.2) MUTATED 16 8.4 (1.0)
AMP PEAK 17(15Q11.2) WILD-TYPE 476 7.6 (1.0)

Figure S105.  Get High-res Image Gene #17: 'amp_15q11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_16q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.0266 (Wilcoxon-test), Q value = 0.082

Table S106.  Gene #18: 'amp_16q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 18(16Q11.2) MUTATED 28 63.6 (6.2)
AMP PEAK 18(16Q11.2) WILD-TYPE 453 60.8 (6.8)

Figure S106.  Get High-res Image Gene #18: 'amp_16q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_16q11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00025 (Fisher's exact test), Q value = 0.0023

Table S107.  Gene #18: 'amp_16q11.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 18(16Q11.2) MUTATED 2 27 1
AMP PEAK 18(16Q11.2) WILD-TYPE 185 261 9

Figure S107.  Get High-res Image Gene #18: 'amp_16q11.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_16q11.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0724 (Fisher's exact test), Q value = 0.17

Table S108.  Gene #18: 'amp_16q11.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 18(16Q11.2) MUTATED 19 9
AMP PEAK 18(16Q11.2) WILD-TYPE 324 68

Figure S108.  Get High-res Image Gene #18: 'amp_16q11.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_16q11.2' versus 'RADIATION_THERAPY'

P value = 0.102 (Fisher's exact test), Q value = 0.22

Table S109.  Gene #18: 'amp_16q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
AMP PEAK 18(16Q11.2) MUTATED 17 6
AMP PEAK 18(16Q11.2) WILD-TYPE 373 53

Figure S109.  Get High-res Image Gene #18: 'amp_16q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_16q11.2' versus 'RESIDUAL_TUMOR'

P value = 0.0388 (Fisher's exact test), Q value = 0.11

Table S110.  Gene #18: 'amp_16q11.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 18(16Q11.2) MUTATED 13 16 0 1
AMP PEAK 18(16Q11.2) WILD-TYPE 300 128 5 14

Figure S110.  Get High-res Image Gene #18: 'amp_16q11.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_16q11.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0631 (Wilcoxon-test), Q value = 0.15

Table S111.  Gene #18: 'amp_16q11.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 18(16Q11.2) MUTATED 27 0.7 (1.6)
AMP PEAK 18(16Q11.2) WILD-TYPE 375 0.4 (1.3)

Figure S111.  Get High-res Image Gene #18: 'amp_16q11.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_16q11.2' versus 'GLEASON_SCORE'

P value = 1.71e-06 (Wilcoxon-test), Q value = 5.1e-05

Table S112.  Gene #18: 'amp_16q11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 18(16Q11.2) MUTATED 30 8.5 (0.9)
AMP PEAK 18(16Q11.2) WILD-TYPE 462 7.6 (1.0)

Figure S112.  Get High-res Image Gene #18: 'amp_16q11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_16q11.2' versus 'PSA_VALUE'

P value = 0.0183 (Wilcoxon-test), Q value = 0.061

Table S113.  Gene #18: 'amp_16q11.2' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
AMP PEAK 18(16Q11.2) MUTATED 25 1.3 (2.5)
AMP PEAK 18(16Q11.2) WILD-TYPE 410 1.8 (16.4)

Figure S113.  Get High-res Image Gene #18: 'amp_16q11.2' versus Clinical Feature #10: 'PSA_VALUE'

'amp_17p11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00279 (Fisher's exact test), Q value = 0.014

Table S114.  Gene #19: 'amp_17p11.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 19(17P11.2) MUTATED 4 15 3
AMP PEAK 19(17P11.2) WILD-TYPE 183 273 7

Figure S114.  Get High-res Image Gene #19: 'amp_17p11.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_17p11.2' versus 'PATHOLOGY_N_STAGE'

P value = 8.94e-05 (Fisher's exact test), Q value = 0.00098

Table S115.  Gene #19: 'amp_17p11.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 19(17P11.2) MUTATED 10 12
AMP PEAK 19(17P11.2) WILD-TYPE 333 65

Figure S115.  Get High-res Image Gene #19: 'amp_17p11.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_17p11.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 2.43e-06 (Wilcoxon-test), Q value = 6.7e-05

Table S116.  Gene #19: 'amp_17p11.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 19(17P11.2) MUTATED 21 1.6 (2.6)
AMP PEAK 19(17P11.2) WILD-TYPE 381 0.4 (1.2)

Figure S116.  Get High-res Image Gene #19: 'amp_17p11.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_17p11.2' versus 'GLEASON_SCORE'

P value = 0.000804 (Wilcoxon-test), Q value = 0.0052

Table S117.  Gene #19: 'amp_17p11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 19(17P11.2) MUTATED 22 8.4 (1.1)
AMP PEAK 19(17P11.2) WILD-TYPE 470 7.6 (1.0)

Figure S117.  Get High-res Image Gene #19: 'amp_17p11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_17q23.2' versus 'Time to Death'

P value = 0.115 (logrank test), Q value = 0.24

Table S118.  Gene #20: 'amp_17q23.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 492 9 0.8 - 165.2 (30.6)
AMP PEAK 20(17Q23.2) MUTATED 25 1 4.3 - 109.2 (22.0)
AMP PEAK 20(17Q23.2) WILD-TYPE 467 8 0.8 - 165.2 (30.9)

Figure S118.  Get High-res Image Gene #20: 'amp_17q23.2' versus Clinical Feature #1: 'Time to Death'

'amp_17q23.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00091 (Fisher's exact test), Q value = 0.0057

Table S119.  Gene #20: 'amp_17q23.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 20(17Q23.2) MUTATED 2 20 2
AMP PEAK 20(17Q23.2) WILD-TYPE 185 268 8

Figure S119.  Get High-res Image Gene #20: 'amp_17q23.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_17q23.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0216 (Fisher's exact test), Q value = 0.07

Table S120.  Gene #20: 'amp_17q23.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 20(17Q23.2) MUTATED 14 9
AMP PEAK 20(17Q23.2) WILD-TYPE 329 68

Figure S120.  Get High-res Image Gene #20: 'amp_17q23.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_17q23.2' versus 'RADIATION_THERAPY'

P value = 0.0547 (Fisher's exact test), Q value = 0.14

Table S121.  Gene #20: 'amp_17q23.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
AMP PEAK 20(17Q23.2) MUTATED 16 6
AMP PEAK 20(17Q23.2) WILD-TYPE 374 53

Figure S121.  Get High-res Image Gene #20: 'amp_17q23.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_17q23.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0291 (Fisher's exact test), Q value = 0.087

Table S122.  Gene #20: 'amp_17q23.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients PROSTATE ADENOCARCINOMA ACINAR TYPE PROSTATE ADENOCARCINOMA, OTHER SUBTYPE
ALL 478 14
AMP PEAK 20(17Q23.2) MUTATED 22 3
AMP PEAK 20(17Q23.2) WILD-TYPE 456 11

Figure S122.  Get High-res Image Gene #20: 'amp_17q23.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_17q23.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.012 (Wilcoxon-test), Q value = 0.044

Table S123.  Gene #20: 'amp_17q23.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 20(17Q23.2) MUTATED 23 0.7 (0.9)
AMP PEAK 20(17Q23.2) WILD-TYPE 379 0.4 (1.4)

Figure S123.  Get High-res Image Gene #20: 'amp_17q23.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_17q23.2' versus 'GLEASON_SCORE'

P value = 7.54e-05 (Wilcoxon-test), Q value = 0.00086

Table S124.  Gene #20: 'amp_17q23.2' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 20(17Q23.2) MUTATED 25 8.4 (1.0)
AMP PEAK 20(17Q23.2) WILD-TYPE 467 7.6 (1.0)

Figure S124.  Get High-res Image Gene #20: 'amp_17q23.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_17q23.2' versus 'PSA_VALUE'

P value = 0.0468 (Wilcoxon-test), Q value = 0.12

Table S125.  Gene #20: 'amp_17q23.2' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
AMP PEAK 20(17Q23.2) MUTATED 22 15.6 (68.7)
AMP PEAK 20(17Q23.2) WILD-TYPE 413 1.0 (4.1)

Figure S125.  Get High-res Image Gene #20: 'amp_17q23.2' versus Clinical Feature #10: 'PSA_VALUE'

'amp_18q21.31' versus 'Time to Death'

P value = 0.0702 (logrank test), Q value = 0.17

Table S126.  Gene #21: 'amp_18q21.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 492 9 0.8 - 165.2 (30.6)
AMP PEAK 21(18Q21.31) MUTATED 13 1 4.3 - 75.9 (42.8)
AMP PEAK 21(18Q21.31) WILD-TYPE 479 8 0.8 - 165.2 (30.6)

Figure S126.  Get High-res Image Gene #21: 'amp_18q21.31' versus Clinical Feature #1: 'Time to Death'

'amp_18q21.31' versus 'YEARS_TO_BIRTH'

P value = 0.00215 (Wilcoxon-test), Q value = 0.011

Table S127.  Gene #21: 'amp_18q21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 21(18Q21.31) MUTATED 12 66.5 (4.3)
AMP PEAK 21(18Q21.31) WILD-TYPE 469 60.8 (6.8)

Figure S127.  Get High-res Image Gene #21: 'amp_18q21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_18q21.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.00528 (Fisher's exact test), Q value = 0.022

Table S128.  Gene #21: 'amp_18q21.31' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 21(18Q21.31) MUTATED 0 13 0
AMP PEAK 21(18Q21.31) WILD-TYPE 187 275 10

Figure S128.  Get High-res Image Gene #21: 'amp_18q21.31' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_18q21.31' versus 'HISTOLOGICAL_TYPE'

P value = 0.0491 (Fisher's exact test), Q value = 0.13

Table S129.  Gene #21: 'amp_18q21.31' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients PROSTATE ADENOCARCINOMA ACINAR TYPE PROSTATE ADENOCARCINOMA, OTHER SUBTYPE
ALL 478 14
AMP PEAK 21(18Q21.31) MUTATED 11 2
AMP PEAK 21(18Q21.31) WILD-TYPE 467 12

Figure S129.  Get High-res Image Gene #21: 'amp_18q21.31' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_18q21.31' versus 'GLEASON_SCORE'

P value = 0.00501 (Wilcoxon-test), Q value = 0.022

Table S130.  Gene #21: 'amp_18q21.31' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 21(18Q21.31) MUTATED 13 8.4 (0.9)
AMP PEAK 21(18Q21.31) WILD-TYPE 479 7.6 (1.0)

Figure S130.  Get High-res Image Gene #21: 'amp_18q21.31' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_19q13.43' versus 'YEARS_TO_BIRTH'

P value = 0.0263 (Wilcoxon-test), Q value = 0.082

Table S131.  Gene #22: 'amp_19q13.43' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 22(19Q13.43) MUTATED 18 64.4 (6.6)
AMP PEAK 22(19Q13.43) WILD-TYPE 463 60.8 (6.8)

Figure S131.  Get High-res Image Gene #22: 'amp_19q13.43' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19q13.43' versus 'PATHOLOGY_T_STAGE'

P value = 0.00035 (Fisher's exact test), Q value = 0.0028

Table S132.  Gene #22: 'amp_19q13.43' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 22(19Q13.43) MUTATED 0 17 1
AMP PEAK 22(19Q13.43) WILD-TYPE 187 271 9

Figure S132.  Get High-res Image Gene #22: 'amp_19q13.43' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_19q13.43' versus 'PATHOLOGY_N_STAGE'

P value = 0.0304 (Fisher's exact test), Q value = 0.089

Table S133.  Gene #22: 'amp_19q13.43' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 22(19Q13.43) MUTATED 11 7
AMP PEAK 22(19Q13.43) WILD-TYPE 332 70

Figure S133.  Get High-res Image Gene #22: 'amp_19q13.43' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_19q13.43' versus 'HISTOLOGICAL_TYPE'

P value = 0.0975 (Fisher's exact test), Q value = 0.21

Table S134.  Gene #22: 'amp_19q13.43' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients PROSTATE ADENOCARCINOMA ACINAR TYPE PROSTATE ADENOCARCINOMA, OTHER SUBTYPE
ALL 478 14
AMP PEAK 22(19Q13.43) MUTATED 17 2
AMP PEAK 22(19Q13.43) WILD-TYPE 461 12

Figure S134.  Get High-res Image Gene #22: 'amp_19q13.43' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_19q13.43' versus 'RESIDUAL_TUMOR'

P value = 0.12 (Fisher's exact test), Q value = 0.25

Table S135.  Gene #22: 'amp_19q13.43' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 22(19Q13.43) MUTATED 8 10 0 0
AMP PEAK 22(19Q13.43) WILD-TYPE 305 134 5 15

Figure S135.  Get High-res Image Gene #22: 'amp_19q13.43' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_19q13.43' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00407 (Wilcoxon-test), Q value = 0.018

Table S136.  Gene #22: 'amp_19q13.43' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 22(19Q13.43) MUTATED 18 1.1 (2.0)
AMP PEAK 22(19Q13.43) WILD-TYPE 384 0.4 (1.3)

Figure S136.  Get High-res Image Gene #22: 'amp_19q13.43' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_19q13.43' versus 'GLEASON_SCORE'

P value = 3.73e-06 (Wilcoxon-test), Q value = 9.2e-05

Table S137.  Gene #22: 'amp_19q13.43' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 22(19Q13.43) MUTATED 19 8.7 (0.9)
AMP PEAK 22(19Q13.43) WILD-TYPE 473 7.6 (1.0)

Figure S137.  Get High-res Image Gene #22: 'amp_19q13.43' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_20q13.2' versus 'YEARS_TO_BIRTH'

P value = 0.00432 (Wilcoxon-test), Q value = 0.019

Table S138.  Gene #23: 'amp_20q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 23(20Q13.2) MUTATED 42 63.7 (4.5)
AMP PEAK 23(20Q13.2) WILD-TYPE 439 60.7 (6.9)

Figure S138.  Get High-res Image Gene #23: 'amp_20q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_20q13.2' versus 'PATHOLOGY_T_STAGE'

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

Table S139.  Gene #23: 'amp_20q13.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 23(20Q13.2) MUTATED 4 37 3
AMP PEAK 23(20Q13.2) WILD-TYPE 183 251 7

Figure S139.  Get High-res Image Gene #23: 'amp_20q13.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_20q13.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00992 (Fisher's exact test), Q value = 0.038

Table S140.  Gene #23: 'amp_20q13.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 23(20Q13.2) MUTATED 27 14
AMP PEAK 23(20Q13.2) WILD-TYPE 316 63

Figure S140.  Get High-res Image Gene #23: 'amp_20q13.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_20q13.2' versus 'RADIATION_THERAPY'

P value = 0.0832 (Fisher's exact test), Q value = 0.18

Table S141.  Gene #23: 'amp_20q13.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
AMP PEAK 23(20Q13.2) MUTATED 31 9
AMP PEAK 23(20Q13.2) WILD-TYPE 359 50

Figure S141.  Get High-res Image Gene #23: 'amp_20q13.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_20q13.2' versus 'RESIDUAL_TUMOR'

P value = 0.012 (Fisher's exact test), Q value = 0.044

Table S142.  Gene #23: 'amp_20q13.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 23(20Q13.2) MUTATED 19 22 0 2
AMP PEAK 23(20Q13.2) WILD-TYPE 294 122 5 13

Figure S142.  Get High-res Image Gene #23: 'amp_20q13.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_20q13.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00157 (Wilcoxon-test), Q value = 0.0088

Table S143.  Gene #23: 'amp_20q13.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 23(20Q13.2) MUTATED 39 0.8 (1.5)
AMP PEAK 23(20Q13.2) WILD-TYPE 363 0.4 (1.3)

Figure S143.  Get High-res Image Gene #23: 'amp_20q13.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_20q13.2' versus 'GLEASON_SCORE'

P value = 7.21e-08 (Wilcoxon-test), Q value = 2.9e-06

Table S144.  Gene #23: 'amp_20q13.2' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 23(20Q13.2) MUTATED 45 8.4 (1.0)
AMP PEAK 23(20Q13.2) WILD-TYPE 447 7.5 (1.0)

Figure S144.  Get High-res Image Gene #23: 'amp_20q13.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_20q13.2' versus 'PSA_VALUE'

P value = 0.073 (Wilcoxon-test), Q value = 0.17

Table S145.  Gene #23: 'amp_20q13.2' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
AMP PEAK 23(20Q13.2) MUTATED 44 8.4 (48.6)
AMP PEAK 23(20Q13.2) WILD-TYPE 391 1.0 (4.2)

Figure S145.  Get High-res Image Gene #23: 'amp_20q13.2' versus Clinical Feature #10: 'PSA_VALUE'

'amp_xp22.2' versus 'YEARS_TO_BIRTH'

P value = 0.016 (Wilcoxon-test), Q value = 0.056

Table S146.  Gene #24: 'amp_xp22.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 24(XP22.2) MUTATED 25 64.0 (6.0)
AMP PEAK 24(XP22.2) WILD-TYPE 456 60.8 (6.8)

Figure S146.  Get High-res Image Gene #24: 'amp_xp22.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xp22.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00179 (Fisher's exact test), Q value = 0.0096

Table S147.  Gene #24: 'amp_xp22.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 24(XP22.2) MUTATED 3 22 2
AMP PEAK 24(XP22.2) WILD-TYPE 184 266 8

Figure S147.  Get High-res Image Gene #24: 'amp_xp22.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_xp22.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0359 (Fisher's exact test), Q value = 0.1

Table S148.  Gene #24: 'amp_xp22.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 24(XP22.2) MUTATED 17 9
AMP PEAK 24(XP22.2) WILD-TYPE 326 68

Figure S148.  Get High-res Image Gene #24: 'amp_xp22.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_xp22.2' versus 'RESIDUAL_TUMOR'

P value = 0.00092 (Fisher's exact test), Q value = 0.0057

Table S149.  Gene #24: 'amp_xp22.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 24(XP22.2) MUTATED 8 16 1 1
AMP PEAK 24(XP22.2) WILD-TYPE 305 128 4 14

Figure S149.  Get High-res Image Gene #24: 'amp_xp22.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_xp22.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00664 (Wilcoxon-test), Q value = 0.027

Table S150.  Gene #24: 'amp_xp22.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 24(XP22.2) MUTATED 25 0.8 (1.5)
AMP PEAK 24(XP22.2) WILD-TYPE 377 0.4 (1.4)

Figure S150.  Get High-res Image Gene #24: 'amp_xp22.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_xp22.2' versus 'GLEASON_SCORE'

P value = 4.75e-05 (Wilcoxon-test), Q value = 0.00061

Table S151.  Gene #24: 'amp_xp22.2' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 24(XP22.2) MUTATED 27 8.4 (0.8)
AMP PEAK 24(XP22.2) WILD-TYPE 465 7.6 (1.0)

Figure S151.  Get High-res Image Gene #24: 'amp_xp22.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_xp22.2' versus 'PSA_VALUE'

P value = 0.0709 (Wilcoxon-test), Q value = 0.17

Table S152.  Gene #24: 'amp_xp22.2' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
AMP PEAK 24(XP22.2) MUTATED 23 1.1 (2.6)
AMP PEAK 24(XP22.2) WILD-TYPE 412 1.8 (16.4)

Figure S152.  Get High-res Image Gene #24: 'amp_xp22.2' versus Clinical Feature #10: 'PSA_VALUE'

'amp_xq12' versus 'Time to Death'

P value = 0.12 (logrank test), Q value = 0.25

Table S153.  Gene #25: 'amp_xq12' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 492 9 0.8 - 165.2 (30.6)
AMP PEAK 25(XQ12) MUTATED 16 1 4.8 - 63.5 (34.2)
AMP PEAK 25(XQ12) WILD-TYPE 476 8 0.8 - 165.2 (30.5)

Figure S153.  Get High-res Image Gene #25: 'amp_xq12' versus Clinical Feature #1: 'Time to Death'

'amp_xq12' versus 'YEARS_TO_BIRTH'

P value = 0.00298 (Wilcoxon-test), Q value = 0.014

Table S154.  Gene #25: 'amp_xq12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 25(XQ12) MUTATED 15 65.9 (4.5)
AMP PEAK 25(XQ12) WILD-TYPE 466 60.8 (6.8)

Figure S154.  Get High-res Image Gene #25: 'amp_xq12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xq12' versus 'PATHOLOGY_T_STAGE'

P value = 0.00745 (Fisher's exact test), Q value = 0.03

Table S155.  Gene #25: 'amp_xq12' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 25(XQ12) MUTATED 2 11 2
AMP PEAK 25(XQ12) WILD-TYPE 185 277 8

Figure S155.  Get High-res Image Gene #25: 'amp_xq12' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_xq12' versus 'RESIDUAL_TUMOR'

P value = 0.0128 (Fisher's exact test), Q value = 0.046

Table S156.  Gene #25: 'amp_xq12' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 25(XQ12) MUTATED 5 8 1 1
AMP PEAK 25(XQ12) WILD-TYPE 308 136 4 14

Figure S156.  Get High-res Image Gene #25: 'amp_xq12' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_xq12' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0298 (Wilcoxon-test), Q value = 0.088

Table S157.  Gene #25: 'amp_xq12' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 25(XQ12) MUTATED 14 0.9 (1.6)
AMP PEAK 25(XQ12) WILD-TYPE 388 0.4 (1.4)

Figure S157.  Get High-res Image Gene #25: 'amp_xq12' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_xq12' versus 'GLEASON_SCORE'

P value = 7.7e-06 (Wilcoxon-test), Q value = 0.00015

Table S158.  Gene #25: 'amp_xq12' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 25(XQ12) MUTATED 16 8.8 (0.7)
AMP PEAK 25(XQ12) WILD-TYPE 476 7.6 (1.0)

Figure S158.  Get High-res Image Gene #25: 'amp_xq12' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_xq21.1' versus 'YEARS_TO_BIRTH'

P value = 0.0164 (Wilcoxon-test), Q value = 0.056

Table S159.  Gene #26: 'amp_xq21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 26(XQ21.1) MUTATED 14 65.2 (5.1)
AMP PEAK 26(XQ21.1) WILD-TYPE 467 60.9 (6.8)

Figure S159.  Get High-res Image Gene #26: 'amp_xq21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xq21.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0194 (Fisher's exact test), Q value = 0.064

Table S160.  Gene #26: 'amp_xq21.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 26(XQ21.1) MUTATED 3 9 2
AMP PEAK 26(XQ21.1) WILD-TYPE 184 279 8

Figure S160.  Get High-res Image Gene #26: 'amp_xq21.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_xq21.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0274 (Fisher's exact test), Q value = 0.083

Table S161.  Gene #26: 'amp_xq21.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
AMP PEAK 26(XQ21.1) MUTATED 8 6
AMP PEAK 26(XQ21.1) WILD-TYPE 335 71

Figure S161.  Get High-res Image Gene #26: 'amp_xq21.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_xq21.1' versus 'RESIDUAL_TUMOR'

P value = 0.0785 (Fisher's exact test), Q value = 0.18

Table S162.  Gene #26: 'amp_xq21.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 26(XQ21.1) MUTATED 7 5 1 1
AMP PEAK 26(XQ21.1) WILD-TYPE 306 139 4 14

Figure S162.  Get High-res Image Gene #26: 'amp_xq21.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_xq21.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.027 (Wilcoxon-test), Q value = 0.082

Table S163.  Gene #26: 'amp_xq21.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
AMP PEAK 26(XQ21.1) MUTATED 14 0.9 (1.7)
AMP PEAK 26(XQ21.1) WILD-TYPE 388 0.4 (1.3)

Figure S163.  Get High-res Image Gene #26: 'amp_xq21.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_xq21.1' versus 'GLEASON_SCORE'

P value = 0.00216 (Wilcoxon-test), Q value = 0.011

Table S164.  Gene #26: 'amp_xq21.1' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 26(XQ21.1) MUTATED 14 8.4 (0.9)
AMP PEAK 26(XQ21.1) WILD-TYPE 478 7.6 (1.0)

Figure S164.  Get High-res Image Gene #26: 'amp_xq21.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_xq21.1' versus 'RACE'

P value = 0.0274 (Fisher's exact test), Q value = 0.083

Table S165.  Gene #26: 'amp_xq21.1' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 7 146
AMP PEAK 26(XQ21.1) MUTATED 0 2 3
AMP PEAK 26(XQ21.1) WILD-TYPE 2 5 143

Figure S165.  Get High-res Image Gene #26: 'amp_xq21.1' versus Clinical Feature #11: 'RACE'

'amp_xq21.31' versus 'YEARS_TO_BIRTH'

P value = 0.0336 (Wilcoxon-test), Q value = 0.096

Table S166.  Gene #27: 'amp_xq21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
AMP PEAK 27(XQ21.31) MUTATED 12 65.0 (5.2)
AMP PEAK 27(XQ21.31) WILD-TYPE 469 60.9 (6.8)

Figure S166.  Get High-res Image Gene #27: 'amp_xq21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xq21.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.0714 (Fisher's exact test), Q value = 0.17

Table S167.  Gene #27: 'amp_xq21.31' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 27(XQ21.31) MUTATED 2 10 1
AMP PEAK 27(XQ21.31) WILD-TYPE 185 278 9

Figure S167.  Get High-res Image Gene #27: 'amp_xq21.31' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_xq21.31' versus 'RESIDUAL_TUMOR'

P value = 0.0813 (Fisher's exact test), Q value = 0.18

Table S168.  Gene #27: 'amp_xq21.31' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
AMP PEAK 27(XQ21.31) MUTATED 6 6 1 0
AMP PEAK 27(XQ21.31) WILD-TYPE 307 138 4 15

Figure S168.  Get High-res Image Gene #27: 'amp_xq21.31' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_xq21.31' versus 'GLEASON_SCORE'

P value = 0.0035 (Wilcoxon-test), Q value = 0.016

Table S169.  Gene #27: 'amp_xq21.31' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 27(XQ21.31) MUTATED 13 8.5 (1.1)
AMP PEAK 27(XQ21.31) WILD-TYPE 479 7.6 (1.0)

Figure S169.  Get High-res Image Gene #27: 'amp_xq21.31' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_xq21.31' versus 'PSA_VALUE'

P value = 0.0697 (Wilcoxon-test), Q value = 0.17

Table S170.  Gene #27: 'amp_xq21.31' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
AMP PEAK 27(XQ21.31) MUTATED 11 1.6 (3.6)
AMP PEAK 27(XQ21.31) WILD-TYPE 424 1.8 (16.1)

Figure S170.  Get High-res Image Gene #27: 'amp_xq21.31' versus Clinical Feature #10: 'PSA_VALUE'

'amp_xq25' versus 'PATHOLOGY_T_STAGE'

P value = 0.0512 (Fisher's exact test), Q value = 0.13

Table S171.  Gene #28: 'amp_xq25' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
AMP PEAK 28(XQ25) MUTATED 5 11 2
AMP PEAK 28(XQ25) WILD-TYPE 182 277 8

Figure S171.  Get High-res Image Gene #28: 'amp_xq25' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_xq25' versus 'GLEASON_SCORE'

P value = 0.00516 (Wilcoxon-test), Q value = 0.022

Table S172.  Gene #28: 'amp_xq25' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
AMP PEAK 28(XQ25) MUTATED 19 8.3 (1.0)
AMP PEAK 28(XQ25) WILD-TYPE 473 7.6 (1.0)

Figure S172.  Get High-res Image Gene #28: 'amp_xq25' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_xq25' versus 'RACE'

P value = 0.0178 (Fisher's exact test), Q value = 0.06

Table S173.  Gene #28: 'amp_xq25' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 7 146
AMP PEAK 28(XQ25) MUTATED 1 1 4
AMP PEAK 28(XQ25) WILD-TYPE 1 6 142

Figure S173.  Get High-res Image Gene #28: 'amp_xq25' versus Clinical Feature #11: 'RACE'

'del_1p31.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00987 (Fisher's exact test), Q value = 0.038

Table S174.  Gene #29: 'del_1p31.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 1(1P31.3) MUTATED 13 45 2
DEL PEAK 1(1P31.3) WILD-TYPE 174 243 8

Figure S174.  Get High-res Image Gene #29: 'del_1p31.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_1p31.3' versus 'RADIATION_THERAPY'

P value = 0.0505 (Fisher's exact test), Q value = 0.13

Table S175.  Gene #29: 'del_1p31.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 1(1P31.3) MUTATED 42 12
DEL PEAK 1(1P31.3) WILD-TYPE 348 47

Figure S175.  Get High-res Image Gene #29: 'del_1p31.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_1p31.3' versus 'RESIDUAL_TUMOR'

P value = 0.0491 (Fisher's exact test), Q value = 0.13

Table S176.  Gene #29: 'del_1p31.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 1(1P31.3) MUTATED 30 26 1 2
DEL PEAK 1(1P31.3) WILD-TYPE 283 118 4 13

Figure S176.  Get High-res Image Gene #29: 'del_1p31.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_1p31.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0618 (Wilcoxon-test), Q value = 0.15

Table S177.  Gene #29: 'del_1p31.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 1(1P31.3) MUTATED 52 0.6 (1.1)
DEL PEAK 1(1P31.3) WILD-TYPE 350 0.4 (1.4)

Figure S177.  Get High-res Image Gene #29: 'del_1p31.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_1p31.3' versus 'GLEASON_SCORE'

P value = 0.00012 (Wilcoxon-test), Q value = 0.0013

Table S178.  Gene #29: 'del_1p31.3' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 1(1P31.3) MUTATED 60 8.1 (1.1)
DEL PEAK 1(1P31.3) WILD-TYPE 432 7.5 (1.0)

Figure S178.  Get High-res Image Gene #29: 'del_1p31.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_1p22.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00263 (Fisher's exact test), Q value = 0.013

Table S179.  Gene #30: 'del_1p22.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 2(1P22.1) MUTATED 11 44 2
DEL PEAK 2(1P22.1) WILD-TYPE 176 244 8

Figure S179.  Get High-res Image Gene #30: 'del_1p22.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_1p22.1' versus 'RESIDUAL_TUMOR'

P value = 0.108 (Fisher's exact test), Q value = 0.23

Table S180.  Gene #30: 'del_1p22.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 2(1P22.1) MUTATED 30 20 0 4
DEL PEAK 2(1P22.1) WILD-TYPE 283 124 5 11

Figure S180.  Get High-res Image Gene #30: 'del_1p22.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_1p22.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0477 (Wilcoxon-test), Q value = 0.13

Table S181.  Gene #30: 'del_1p22.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 2(1P22.1) MUTATED 47 0.6 (1.3)
DEL PEAK 2(1P22.1) WILD-TYPE 355 0.4 (1.4)

Figure S181.  Get High-res Image Gene #30: 'del_1p22.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_1p22.1' versus 'GLEASON_SCORE'

P value = 0.000145 (Wilcoxon-test), Q value = 0.0014

Table S182.  Gene #30: 'del_1p22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 2(1P22.1) MUTATED 58 8.1 (1.0)
DEL PEAK 2(1P22.1) WILD-TYPE 434 7.5 (1.0)

Figure S182.  Get High-res Image Gene #30: 'del_1p22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_1q42.3' versus 'Time to Death'

P value = 0.000142 (logrank test), Q value = 0.0014

Table S183.  Gene #32: 'del_1q42.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 492 9 0.8 - 165.2 (30.6)
DEL PEAK 4(1Q42.3) MUTATED 47 5 1.0 - 122.2 (35.8)
DEL PEAK 4(1Q42.3) WILD-TYPE 445 4 0.8 - 165.2 (30.6)

Figure S183.  Get High-res Image Gene #32: 'del_1q42.3' versus Clinical Feature #1: 'Time to Death'

'del_1q42.3' versus 'YEARS_TO_BIRTH'

P value = 0.116 (Wilcoxon-test), Q value = 0.24

Table S184.  Gene #32: 'del_1q42.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
DEL PEAK 4(1Q42.3) MUTATED 47 62.4 (6.3)
DEL PEAK 4(1Q42.3) WILD-TYPE 434 60.8 (6.8)

Figure S184.  Get High-res Image Gene #32: 'del_1q42.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1q42.3' versus 'RESIDUAL_TUMOR'

P value = 0.0162 (Fisher's exact test), Q value = 0.056

Table S185.  Gene #32: 'del_1q42.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 4(1Q42.3) MUTATED 21 23 0 2
DEL PEAK 4(1Q42.3) WILD-TYPE 292 121 5 13

Figure S185.  Get High-res Image Gene #32: 'del_1q42.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_1q42.3' versus 'GLEASON_SCORE'

P value = 0.0713 (Wilcoxon-test), Q value = 0.17

Table S186.  Gene #32: 'del_1q42.3' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 4(1Q42.3) MUTATED 47 7.9 (1.0)
DEL PEAK 4(1Q42.3) WILD-TYPE 445 7.6 (1.0)

Figure S186.  Get High-res Image Gene #32: 'del_1q42.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_1q42.3' versus 'PSA_VALUE'

P value = 0.0864 (Wilcoxon-test), Q value = 0.19

Table S187.  Gene #32: 'del_1q42.3' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
DEL PEAK 4(1Q42.3) MUTATED 39 2.5 (7.3)
DEL PEAK 4(1Q42.3) WILD-TYPE 396 1.7 (16.6)

Figure S187.  Get High-res Image Gene #32: 'del_1q42.3' versus Clinical Feature #10: 'PSA_VALUE'

'del_2p21' versus 'PATHOLOGY_T_STAGE'

P value = 0.00041 (Fisher's exact test), Q value = 0.0032

Table S188.  Gene #33: 'del_2p21' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 5(2P21) MUTATED 7 36 3
DEL PEAK 5(2P21) WILD-TYPE 180 252 7

Figure S188.  Get High-res Image Gene #33: 'del_2p21' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_2p21' versus 'PATHOLOGY_N_STAGE'

P value = 0.0612 (Fisher's exact test), Q value = 0.15

Table S189.  Gene #33: 'del_2p21' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 5(2P21) MUTATED 31 13
DEL PEAK 5(2P21) WILD-TYPE 312 64

Figure S189.  Get High-res Image Gene #33: 'del_2p21' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_2p21' versus 'RESIDUAL_TUMOR'

P value = 0.0363 (Fisher's exact test), Q value = 0.1

Table S190.  Gene #33: 'del_2p21' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 5(2P21) MUTATED 21 20 1 2
DEL PEAK 5(2P21) WILD-TYPE 292 124 4 13

Figure S190.  Get High-res Image Gene #33: 'del_2p21' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_2p21' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0315 (Wilcoxon-test), Q value = 0.091

Table S191.  Gene #33: 'del_2p21' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 5(2P21) MUTATED 43 0.6 (1.3)
DEL PEAK 5(2P21) WILD-TYPE 359 0.4 (1.4)

Figure S191.  Get High-res Image Gene #33: 'del_2p21' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_2p21' versus 'GLEASON_SCORE'

P value = 0.00178 (Wilcoxon-test), Q value = 0.0096

Table S192.  Gene #33: 'del_2p21' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 5(2P21) MUTATED 46 8.1 (1.0)
DEL PEAK 5(2P21) WILD-TYPE 446 7.6 (1.0)

Figure S192.  Get High-res Image Gene #33: 'del_2p21' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_2q22.1' versus 'YEARS_TO_BIRTH'

P value = 1.94e-05 (Wilcoxon-test), Q value = 0.00028

Table S193.  Gene #34: 'del_2q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
DEL PEAK 6(2Q22.1) MUTATED 91 63.6 (5.8)
DEL PEAK 6(2Q22.1) WILD-TYPE 390 60.4 (6.9)

Figure S193.  Get High-res Image Gene #34: 'del_2q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2q22.1' versus 'GLEASON_SCORE'

P value = 0.0098 (Wilcoxon-test), Q value = 0.038

Table S194.  Gene #34: 'del_2q22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 6(2Q22.1) MUTATED 92 7.9 (1.0)
DEL PEAK 6(2Q22.1) WILD-TYPE 400 7.6 (1.0)

Figure S194.  Get High-res Image Gene #34: 'del_2q22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_2q22.3' versus 'YEARS_TO_BIRTH'

P value = 0.00296 (Wilcoxon-test), Q value = 0.014

Table S195.  Gene #35: 'del_2q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
DEL PEAK 7(2Q22.3) MUTATED 84 62.9 (6.4)
DEL PEAK 7(2Q22.3) WILD-TYPE 397 60.6 (6.8)

Figure S195.  Get High-res Image Gene #35: 'del_2q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2q22.3' versus 'GLEASON_SCORE'

P value = 0.0726 (Wilcoxon-test), Q value = 0.17

Table S196.  Gene #35: 'del_2q22.3' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 7(2Q22.3) MUTATED 85 7.8 (1.1)
DEL PEAK 7(2Q22.3) WILD-TYPE 407 7.6 (1.0)

Figure S196.  Get High-res Image Gene #35: 'del_2q22.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_3p13' versus 'YEARS_TO_BIRTH'

P value = 0.0501 (Wilcoxon-test), Q value = 0.13

Table S197.  Gene #36: 'del_3p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
DEL PEAK 8(3P13) MUTATED 78 59.7 (7.4)
DEL PEAK 8(3P13) WILD-TYPE 403 61.2 (6.7)

Figure S197.  Get High-res Image Gene #36: 'del_3p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_3p13' versus 'RADIATION_THERAPY'

P value = 0.0814 (Fisher's exact test), Q value = 0.18

Table S198.  Gene #36: 'del_3p13' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 8(3P13) MUTATED 56 14
DEL PEAK 8(3P13) WILD-TYPE 334 45

Figure S198.  Get High-res Image Gene #36: 'del_3p13' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_3q29' versus 'GLEASON_SCORE'

P value = 0.113 (Wilcoxon-test), Q value = 0.24

Table S199.  Gene #37: 'del_3q29' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 9(3Q29) MUTATED 32 7.9 (1.1)
DEL PEAK 9(3Q29) WILD-TYPE 460 7.6 (1.0)

Figure S199.  Get High-res Image Gene #37: 'del_3q29' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_4q28.2' versus 'YEARS_TO_BIRTH'

P value = 0.00139 (Wilcoxon-test), Q value = 0.008

Table S200.  Gene #38: 'del_4q28.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
DEL PEAK 10(4Q28.2) MUTATED 50 63.9 (6.0)
DEL PEAK 10(4Q28.2) WILD-TYPE 431 60.6 (6.8)

Figure S200.  Get High-res Image Gene #38: 'del_4q28.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q28.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0561 (Fisher's exact test), Q value = 0.14

Table S201.  Gene #38: 'del_4q28.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 10(4Q28.2) MUTATED 15 33 3
DEL PEAK 10(4Q28.2) WILD-TYPE 172 255 7

Figure S201.  Get High-res Image Gene #38: 'del_4q28.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_4q28.2' versus 'RADIATION_THERAPY'

P value = 0.118 (Fisher's exact test), Q value = 0.25

Table S202.  Gene #38: 'del_4q28.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 10(4Q28.2) MUTATED 39 10
DEL PEAK 10(4Q28.2) WILD-TYPE 351 49

Figure S202.  Get High-res Image Gene #38: 'del_4q28.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_4q28.2' versus 'GLEASON_SCORE'

P value = 0.000447 (Wilcoxon-test), Q value = 0.0034

Table S203.  Gene #38: 'del_4q28.2' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 10(4Q28.2) MUTATED 51 8.1 (1.0)
DEL PEAK 10(4Q28.2) WILD-TYPE 441 7.6 (1.0)

Figure S203.  Get High-res Image Gene #38: 'del_4q28.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_5q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.0429 (Wilcoxon-test), Q value = 0.12

Table S204.  Gene #39: 'del_5q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
DEL PEAK 11(5Q11.2) MUTATED 105 62.2 (6.2)
DEL PEAK 11(5Q11.2) WILD-TYPE 376 60.6 (6.9)

Figure S204.  Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_5q11.2' versus 'PATHOLOGY_T_STAGE'

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

Table S205.  Gene #39: 'del_5q11.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 11(5Q11.2) MUTATED 17 81 5
DEL PEAK 11(5Q11.2) WILD-TYPE 170 207 5

Figure S205.  Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_5q11.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.000458 (Fisher's exact test), Q value = 0.0034

Table S206.  Gene #39: 'del_5q11.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 11(5Q11.2) MUTATED 66 30
DEL PEAK 11(5Q11.2) WILD-TYPE 277 47

Figure S206.  Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_5q11.2' versus 'RADIATION_THERAPY'

P value = 0.0266 (Fisher's exact test), Q value = 0.082

Table S207.  Gene #39: 'del_5q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 11(5Q11.2) MUTATED 78 20
DEL PEAK 11(5Q11.2) WILD-TYPE 312 39

Figure S207.  Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_5q11.2' versus 'RESIDUAL_TUMOR'

P value = 0.0363 (Fisher's exact test), Q value = 0.1

Table S208.  Gene #39: 'del_5q11.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 11(5Q11.2) MUTATED 54 41 1 4
DEL PEAK 11(5Q11.2) WILD-TYPE 259 103 4 11

Figure S208.  Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_5q11.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 8.86e-06 (Wilcoxon-test), Q value = 0.00015

Table S209.  Gene #39: 'del_5q11.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 11(5Q11.2) MUTATED 88 1.0 (2.2)
DEL PEAK 11(5Q11.2) WILD-TYPE 314 0.3 (1.0)

Figure S209.  Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_5q11.2' versus 'GLEASON_SCORE'

P value = 1.22e-09 (Wilcoxon-test), Q value = 1e-07

Table S210.  Gene #39: 'del_5q11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 11(5Q11.2) MUTATED 105 8.1 (1.0)
DEL PEAK 11(5Q11.2) WILD-TYPE 387 7.5 (1.0)

Figure S210.  Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_5q13.2' versus 'PATHOLOGY_T_STAGE'

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

Table S211.  Gene #40: 'del_5q13.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 12(5Q13.2) MUTATED 15 78 5
DEL PEAK 12(5Q13.2) WILD-TYPE 172 210 5

Figure S211.  Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_5q13.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0221 (Fisher's exact test), Q value = 0.071

Table S212.  Gene #40: 'del_5q13.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 12(5Q13.2) MUTATED 68 25
DEL PEAK 12(5Q13.2) WILD-TYPE 275 52

Figure S212.  Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_5q13.2' versus 'RADIATION_THERAPY'

P value = 0.0555 (Fisher's exact test), Q value = 0.14

Table S213.  Gene #40: 'del_5q13.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 12(5Q13.2) MUTATED 74 18
DEL PEAK 12(5Q13.2) WILD-TYPE 316 41

Figure S213.  Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_5q13.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00158 (Wilcoxon-test), Q value = 0.0089

Table S214.  Gene #40: 'del_5q13.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 12(5Q13.2) MUTATED 85 1.0 (2.4)
DEL PEAK 12(5Q13.2) WILD-TYPE 317 0.3 (0.8)

Figure S214.  Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_5q13.2' versus 'GLEASON_SCORE'

P value = 5.97e-09 (Wilcoxon-test), Q value = 3.4e-07

Table S215.  Gene #40: 'del_5q13.2' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 12(5Q13.2) MUTATED 99 8.1 (1.0)
DEL PEAK 12(5Q13.2) WILD-TYPE 393 7.5 (1.0)

Figure S215.  Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_5q21.1' versus 'YEARS_TO_BIRTH'

P value = 0.0528 (Wilcoxon-test), Q value = 0.13

Table S216.  Gene #41: 'del_5q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
DEL PEAK 13(5Q21.1) MUTATED 108 62.1 (6.0)
DEL PEAK 13(5Q21.1) WILD-TYPE 373 60.6 (7.0)

Figure S216.  Get High-res Image Gene #41: 'del_5q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_5q21.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0226 (Fisher's exact test), Q value = 0.072

Table S217.  Gene #41: 'del_5q21.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 13(5Q21.1) MUTATED 30 75 3
DEL PEAK 13(5Q21.1) WILD-TYPE 157 213 7

Figure S217.  Get High-res Image Gene #41: 'del_5q21.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_5q21.1' versus 'GLEASON_SCORE'

P value = 0.00132 (Wilcoxon-test), Q value = 0.0077

Table S218.  Gene #41: 'del_5q21.1' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 13(5Q21.1) MUTATED 109 7.9 (1.0)
DEL PEAK 13(5Q21.1) WILD-TYPE 383 7.5 (1.0)

Figure S218.  Get High-res Image Gene #41: 'del_5q21.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_5q21.1' versus 'PSA_VALUE'

P value = 0.0765 (Wilcoxon-test), Q value = 0.17

Table S219.  Gene #41: 'del_5q21.1' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
DEL PEAK 13(5Q21.1) MUTATED 93 5.1 (33.8)
DEL PEAK 13(5Q21.1) WILD-TYPE 342 0.9 (3.5)

Figure S219.  Get High-res Image Gene #41: 'del_5q21.1' versus Clinical Feature #10: 'PSA_VALUE'

'del_6p25.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00975 (Fisher's exact test), Q value = 0.038

Table S220.  Gene #42: 'del_6p25.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 14(6P25.1) MUTATED 10 31 3
DEL PEAK 14(6P25.1) WILD-TYPE 177 257 7

Figure S220.  Get High-res Image Gene #42: 'del_6p25.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_6p25.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00596 (Fisher's exact test), Q value = 0.025

Table S221.  Gene #42: 'del_6p25.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 14(6P25.1) MUTATED 28 15
DEL PEAK 14(6P25.1) WILD-TYPE 315 62

Figure S221.  Get High-res Image Gene #42: 'del_6p25.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_6p25.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0018 (Wilcoxon-test), Q value = 0.0096

Table S222.  Gene #42: 'del_6p25.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 14(6P25.1) MUTATED 39 0.6 (1.0)
DEL PEAK 14(6P25.1) WILD-TYPE 363 0.4 (1.4)

Figure S222.  Get High-res Image Gene #42: 'del_6p25.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_6p25.1' versus 'GLEASON_SCORE'

P value = 9.13e-06 (Wilcoxon-test), Q value = 0.00015

Table S223.  Gene #42: 'del_6p25.1' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 14(6P25.1) MUTATED 46 8.2 (0.9)
DEL PEAK 14(6P25.1) WILD-TYPE 446 7.5 (1.0)

Figure S223.  Get High-res Image Gene #42: 'del_6p25.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_6p25.1' versus 'RACE'

P value = 0.00677 (Fisher's exact test), Q value = 0.027

Table S224.  Gene #42: 'del_6p25.1' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 7 146
DEL PEAK 14(6P25.1) MUTATED 2 1 11
DEL PEAK 14(6P25.1) WILD-TYPE 0 6 135

Figure S224.  Get High-res Image Gene #42: 'del_6p25.1' versus Clinical Feature #11: 'RACE'

'del_6q14.3' versus 'YEARS_TO_BIRTH'

P value = 0.000954 (Wilcoxon-test), Q value = 0.0059

Table S225.  Gene #43: 'del_6q14.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
DEL PEAK 15(6Q14.3) MUTATED 176 62.3 (6.3)
DEL PEAK 15(6Q14.3) WILD-TYPE 305 60.2 (6.9)

Figure S225.  Get High-res Image Gene #43: 'del_6q14.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6q14.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0636 (Fisher's exact test), Q value = 0.15

Table S226.  Gene #43: 'del_6q14.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 15(6Q14.3) MUTATED 57 115 5
DEL PEAK 15(6Q14.3) WILD-TYPE 130 173 5

Figure S226.  Get High-res Image Gene #43: 'del_6q14.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_6q14.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0268 (Fisher's exact test), Q value = 0.082

Table S227.  Gene #43: 'del_6q14.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 15(6Q14.3) MUTATED 121 38
DEL PEAK 15(6Q14.3) WILD-TYPE 222 39

Figure S227.  Get High-res Image Gene #43: 'del_6q14.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_6q14.3' versus 'RESIDUAL_TUMOR'

P value = 0.00045 (Fisher's exact test), Q value = 0.0034

Table S228.  Gene #43: 'del_6q14.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 15(6Q14.3) MUTATED 94 66 2 10
DEL PEAK 15(6Q14.3) WILD-TYPE 219 78 3 5

Figure S228.  Get High-res Image Gene #43: 'del_6q14.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_6q14.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0135 (Wilcoxon-test), Q value = 0.048

Table S229.  Gene #43: 'del_6q14.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 15(6Q14.3) MUTATED 153 0.5 (1.2)
DEL PEAK 15(6Q14.3) WILD-TYPE 249 0.4 (1.4)

Figure S229.  Get High-res Image Gene #43: 'del_6q14.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_6q14.3' versus 'GLEASON_SCORE'

P value = 0.000342 (Wilcoxon-test), Q value = 0.0028

Table S230.  Gene #43: 'del_6q14.3' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 15(6Q14.3) MUTATED 180 7.8 (1.0)
DEL PEAK 15(6Q14.3) WILD-TYPE 312 7.5 (1.0)

Figure S230.  Get High-res Image Gene #43: 'del_6q14.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_8p21.3' versus 'PATHOLOGY_T_STAGE'

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

Table S231.  Gene #44: 'del_8p21.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 16(8P21.3) MUTATED 81 203 8
DEL PEAK 16(8P21.3) WILD-TYPE 106 85 2

Figure S231.  Get High-res Image Gene #44: 'del_8p21.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_8p21.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00273 (Fisher's exact test), Q value = 0.013

Table S232.  Gene #44: 'del_8p21.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 16(8P21.3) MUTATED 199 59
DEL PEAK 16(8P21.3) WILD-TYPE 144 18

Figure S232.  Get High-res Image Gene #44: 'del_8p21.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_8p21.3' versus 'RADIATION_THERAPY'

P value = 0.0639 (Fisher's exact test), Q value = 0.15

Table S233.  Gene #44: 'del_8p21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 16(8P21.3) MUTATED 226 42
DEL PEAK 16(8P21.3) WILD-TYPE 164 17

Figure S233.  Get High-res Image Gene #44: 'del_8p21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_8p21.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00105 (Wilcoxon-test), Q value = 0.0064

Table S234.  Gene #44: 'del_8p21.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 16(8P21.3) MUTATED 246 0.6 (1.6)
DEL PEAK 16(8P21.3) WILD-TYPE 156 0.2 (0.8)

Figure S234.  Get High-res Image Gene #44: 'del_8p21.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_8p21.3' versus 'GLEASON_SCORE'

P value = 0.000927 (Wilcoxon-test), Q value = 0.0057

Table S235.  Gene #44: 'del_8p21.3' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 16(8P21.3) MUTATED 294 7.7 (1.0)
DEL PEAK 16(8P21.3) WILD-TYPE 198 7.4 (1.0)

Figure S235.  Get High-res Image Gene #44: 'del_8p21.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_8p21.3' versus 'PSA_VALUE'

P value = 0.0683 (Wilcoxon-test), Q value = 0.16

Table S236.  Gene #44: 'del_8p21.3' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
DEL PEAK 16(8P21.3) MUTATED 259 2.5 (20.6)
DEL PEAK 16(8P21.3) WILD-TYPE 176 0.6 (2.4)

Figure S236.  Get High-res Image Gene #44: 'del_8p21.3' versus Clinical Feature #10: 'PSA_VALUE'

'del_9p23' versus 'PATHOLOGY_T_STAGE'

P value = 0.0265 (Fisher's exact test), Q value = 0.082

Table S237.  Gene #45: 'del_9p23' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 17(9P23) MUTATED 10 33 2
DEL PEAK 17(9P23) WILD-TYPE 177 255 8

Figure S237.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_9p23' versus 'PATHOLOGY_N_STAGE'

P value = 0.02 (Fisher's exact test), Q value = 0.065

Table S238.  Gene #45: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 17(9P23) MUTATED 29 14
DEL PEAK 17(9P23) WILD-TYPE 314 63

Figure S238.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_9p23' versus 'RADIATION_THERAPY'

P value = 0.0977 (Fisher's exact test), Q value = 0.21

Table S239.  Gene #45: 'del_9p23' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 17(9P23) MUTATED 33 9
DEL PEAK 17(9P23) WILD-TYPE 357 50

Figure S239.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_9p23' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00846 (Wilcoxon-test), Q value = 0.033

Table S240.  Gene #45: 'del_9p23' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 17(9P23) MUTATED 40 0.9 (2.0)
DEL PEAK 17(9P23) WILD-TYPE 362 0.4 (1.3)

Figure S240.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_9p23' versus 'GLEASON_SCORE'

P value = 0.00427 (Wilcoxon-test), Q value = 0.019

Table S241.  Gene #45: 'del_9p23' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 17(9P23) MUTATED 45 8.0 (1.1)
DEL PEAK 17(9P23) WILD-TYPE 447 7.6 (1.0)

Figure S241.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_10q23.31' versus 'PATHOLOGY_T_STAGE'

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

Table S242.  Gene #46: 'del_10q23.31' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 18(10Q23.31) MUTATED 37 113 6
DEL PEAK 18(10Q23.31) WILD-TYPE 150 175 4

Figure S242.  Get High-res Image Gene #46: 'del_10q23.31' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_10q23.31' versus 'PATHOLOGY_N_STAGE'

P value = 0.00352 (Fisher's exact test), Q value = 0.016

Table S243.  Gene #46: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 18(10Q23.31) MUTATED 110 39
DEL PEAK 18(10Q23.31) WILD-TYPE 233 38

Figure S243.  Get High-res Image Gene #46: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_10q23.31' versus 'RADIATION_THERAPY'

P value = 0.0258 (Fisher's exact test), Q value = 0.081

Table S244.  Gene #46: 'del_10q23.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 18(10Q23.31) MUTATED 120 27
DEL PEAK 18(10Q23.31) WILD-TYPE 270 32

Figure S244.  Get High-res Image Gene #46: 'del_10q23.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_10q23.31' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00081 (Wilcoxon-test), Q value = 0.0052

Table S245.  Gene #46: 'del_10q23.31' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 18(10Q23.31) MUTATED 143 0.7 (1.6)
DEL PEAK 18(10Q23.31) WILD-TYPE 259 0.3 (1.2)

Figure S245.  Get High-res Image Gene #46: 'del_10q23.31' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_10q23.31' versus 'GLEASON_SCORE'

P value = 3.5e-08 (Wilcoxon-test), Q value = 1.5e-06

Table S246.  Gene #46: 'del_10q23.31' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 18(10Q23.31) MUTATED 157 8.0 (1.0)
DEL PEAK 18(10Q23.31) WILD-TYPE 335 7.4 (1.0)

Figure S246.  Get High-res Image Gene #46: 'del_10q23.31' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_10q23.31' versus 'PSA_VALUE'

P value = 0.00845 (Wilcoxon-test), Q value = 0.033

Table S247.  Gene #46: 'del_10q23.31' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
DEL PEAK 18(10Q23.31) MUTATED 142 4.2 (27.7)
DEL PEAK 18(10Q23.31) WILD-TYPE 293 0.6 (2.0)

Figure S247.  Get High-res Image Gene #46: 'del_10q23.31' versus Clinical Feature #10: 'PSA_VALUE'

'del_11p11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0192 (Fisher's exact test), Q value = 0.064

Table S248.  Gene #47: 'del_11p11.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 19(11P11.2) MUTATED 6 27 1
DEL PEAK 19(11P11.2) WILD-TYPE 181 261 9

Figure S248.  Get High-res Image Gene #47: 'del_11p11.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_11p11.2' versus 'RESIDUAL_TUMOR'

P value = 0.0444 (Fisher's exact test), Q value = 0.12

Table S249.  Gene #47: 'del_11p11.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 19(11P11.2) MUTATED 15 16 0 2
DEL PEAK 19(11P11.2) WILD-TYPE 298 128 5 13

Figure S249.  Get High-res Image Gene #47: 'del_11p11.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_11p11.2' versus 'GLEASON_SCORE'

P value = 0.0127 (Wilcoxon-test), Q value = 0.046

Table S250.  Gene #47: 'del_11p11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 19(11P11.2) MUTATED 34 8.0 (1.0)
DEL PEAK 19(11P11.2) WILD-TYPE 458 7.6 (1.0)

Figure S250.  Get High-res Image Gene #47: 'del_11p11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_11p11.2' versus 'RACE'

P value = 0.00371 (Fisher's exact test), Q value = 0.017

Table S251.  Gene #47: 'del_11p11.2' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 7 146
DEL PEAK 19(11P11.2) MUTATED 1 2 3
DEL PEAK 19(11P11.2) WILD-TYPE 1 5 143

Figure S251.  Get High-res Image Gene #47: 'del_11p11.2' versus Clinical Feature #11: 'RACE'

'del_11q22.3' versus 'YEARS_TO_BIRTH'

P value = 0.0342 (Wilcoxon-test), Q value = 0.098

Table S252.  Gene #48: 'del_11q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
DEL PEAK 20(11Q22.3) MUTATED 42 63.2 (6.4)
DEL PEAK 20(11Q22.3) WILD-TYPE 439 60.8 (6.8)

Figure S252.  Get High-res Image Gene #48: 'del_11q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q22.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00067 (Fisher's exact test), Q value = 0.0046

Table S253.  Gene #48: 'del_11q22.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 20(11Q22.3) MUTATED 7 33 3
DEL PEAK 20(11Q22.3) WILD-TYPE 180 255 7

Figure S253.  Get High-res Image Gene #48: 'del_11q22.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_11q22.3' versus 'RADIATION_THERAPY'

P value = 0.0606 (Fisher's exact test), Q value = 0.15

Table S254.  Gene #48: 'del_11q22.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 20(11Q22.3) MUTATED 25 8
DEL PEAK 20(11Q22.3) WILD-TYPE 365 51

Figure S254.  Get High-res Image Gene #48: 'del_11q22.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_11q22.3' versus 'RESIDUAL_TUMOR'

P value = 0.00654 (Fisher's exact test), Q value = 0.027

Table S255.  Gene #48: 'del_11q22.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 20(11Q22.3) MUTATED 19 23 0 0
DEL PEAK 20(11Q22.3) WILD-TYPE 294 121 5 15

Figure S255.  Get High-res Image Gene #48: 'del_11q22.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_11q22.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0726 (Wilcoxon-test), Q value = 0.17

Table S256.  Gene #48: 'del_11q22.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 20(11Q22.3) MUTATED 34 0.7 (1.2)
DEL PEAK 20(11Q22.3) WILD-TYPE 368 0.4 (1.4)

Figure S256.  Get High-res Image Gene #48: 'del_11q22.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_11q22.3' versus 'GLEASON_SCORE'

P value = 7.51e-05 (Wilcoxon-test), Q value = 0.00086

Table S257.  Gene #48: 'del_11q22.3' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 20(11Q22.3) MUTATED 43 8.2 (1.0)
DEL PEAK 20(11Q22.3) WILD-TYPE 449 7.6 (1.0)

Figure S257.  Get High-res Image Gene #48: 'del_11q22.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_11q23.2' versus 'YEARS_TO_BIRTH'

P value = 0.0717 (Wilcoxon-test), Q value = 0.17

Table S258.  Gene #49: 'del_11q23.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
DEL PEAK 21(11Q23.2) MUTATED 47 62.7 (6.2)
DEL PEAK 21(11Q23.2) WILD-TYPE 434 60.8 (6.8)

Figure S258.  Get High-res Image Gene #49: 'del_11q23.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q23.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00308 (Fisher's exact test), Q value = 0.015

Table S259.  Gene #49: 'del_11q23.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 21(11Q23.2) MUTATED 11 33 4
DEL PEAK 21(11Q23.2) WILD-TYPE 176 255 6

Figure S259.  Get High-res Image Gene #49: 'del_11q23.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_11q23.2' versus 'RADIATION_THERAPY'

P value = 0.0832 (Fisher's exact test), Q value = 0.18

Table S260.  Gene #49: 'del_11q23.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 21(11Q23.2) MUTATED 31 9
DEL PEAK 21(11Q23.2) WILD-TYPE 359 50

Figure S260.  Get High-res Image Gene #49: 'del_11q23.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_11q23.2' versus 'RESIDUAL_TUMOR'

P value = 0.0225 (Fisher's exact test), Q value = 0.072

Table S261.  Gene #49: 'del_11q23.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 21(11Q23.2) MUTATED 22 23 0 2
DEL PEAK 21(11Q23.2) WILD-TYPE 291 121 5 13

Figure S261.  Get High-res Image Gene #49: 'del_11q23.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_11q23.2' versus 'GLEASON_SCORE'

P value = 9.21e-05 (Wilcoxon-test), Q value = 0.001

Table S262.  Gene #49: 'del_11q23.2' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 21(11Q23.2) MUTATED 48 8.2 (1.0)
DEL PEAK 21(11Q23.2) WILD-TYPE 444 7.5 (1.0)

Figure S262.  Get High-res Image Gene #49: 'del_11q23.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_12p13.1' versus 'PATHOLOGY_T_STAGE'

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

Table S263.  Gene #50: 'del_12p13.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 22(12P13.1) MUTATED 23 95 5
DEL PEAK 22(12P13.1) WILD-TYPE 164 193 5

Figure S263.  Get High-res Image Gene #50: 'del_12p13.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_12p13.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0109 (Fisher's exact test), Q value = 0.041

Table S264.  Gene #50: 'del_12p13.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 22(12P13.1) MUTATED 86 31
DEL PEAK 22(12P13.1) WILD-TYPE 257 46

Figure S264.  Get High-res Image Gene #50: 'del_12p13.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_12p13.1' versus 'RADIATION_THERAPY'

P value = 0.0358 (Fisher's exact test), Q value = 0.1

Table S265.  Gene #50: 'del_12p13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 22(12P13.1) MUTATED 92 22
DEL PEAK 22(12P13.1) WILD-TYPE 298 37

Figure S265.  Get High-res Image Gene #50: 'del_12p13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_12p13.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00366 (Wilcoxon-test), Q value = 0.017

Table S266.  Gene #50: 'del_12p13.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 22(12P13.1) MUTATED 109 0.7 (1.6)
DEL PEAK 22(12P13.1) WILD-TYPE 293 0.3 (1.3)

Figure S266.  Get High-res Image Gene #50: 'del_12p13.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_12p13.1' versus 'GLEASON_SCORE'

P value = 5.32e-05 (Wilcoxon-test), Q value = 0.00066

Table S267.  Gene #50: 'del_12p13.1' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 22(12P13.1) MUTATED 124 7.9 (1.0)
DEL PEAK 22(12P13.1) WILD-TYPE 368 7.5 (1.0)

Figure S267.  Get High-res Image Gene #50: 'del_12p13.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_12p13.1' versus 'PSA_VALUE'

P value = 0.0179 (Wilcoxon-test), Q value = 0.06

Table S268.  Gene #50: 'del_12p13.1' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
DEL PEAK 22(12P13.1) MUTATED 108 1.3 (4.6)
DEL PEAK 22(12P13.1) WILD-TYPE 327 1.9 (18.2)

Figure S268.  Get High-res Image Gene #50: 'del_12p13.1' versus Clinical Feature #10: 'PSA_VALUE'

'del_12q24.32' versus 'PATHOLOGY_T_STAGE'

P value = 0.00318 (Fisher's exact test), Q value = 0.015

Table S269.  Gene #51: 'del_12q24.32' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 23(12Q24.32) MUTATED 7 35 1
DEL PEAK 23(12Q24.32) WILD-TYPE 180 253 9

Figure S269.  Get High-res Image Gene #51: 'del_12q24.32' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_12q24.32' versus 'PATHOLOGY_N_STAGE'

P value = 0.0289 (Fisher's exact test), Q value = 0.087

Table S270.  Gene #51: 'del_12q24.32' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 23(12Q24.32) MUTATED 27 13
DEL PEAK 23(12Q24.32) WILD-TYPE 316 64

Figure S270.  Get High-res Image Gene #51: 'del_12q24.32' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_12q24.32' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0163 (Wilcoxon-test), Q value = 0.056

Table S271.  Gene #51: 'del_12q24.32' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 23(12Q24.32) MUTATED 38 0.9 (2.6)
DEL PEAK 23(12Q24.32) WILD-TYPE 364 0.4 (1.2)

Figure S271.  Get High-res Image Gene #51: 'del_12q24.32' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_12q24.32' versus 'GLEASON_SCORE'

P value = 0.0566 (Wilcoxon-test), Q value = 0.14

Table S272.  Gene #51: 'del_12q24.32' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 23(12Q24.32) MUTATED 43 7.9 (1.0)
DEL PEAK 23(12Q24.32) WILD-TYPE 449 7.6 (1.0)

Figure S272.  Get High-res Image Gene #51: 'del_12q24.32' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_13q14.13' versus 'YEARS_TO_BIRTH'

P value = 0.0136 (Wilcoxon-test), Q value = 0.048

Table S273.  Gene #52: 'del_13q14.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
DEL PEAK 24(13Q14.13) MUTATED 223 61.7 (6.6)
DEL PEAK 24(13Q14.13) WILD-TYPE 258 60.4 (7.0)

Figure S273.  Get High-res Image Gene #52: 'del_13q14.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q14.13' versus 'PATHOLOGY_T_STAGE'

P value = 0.00558 (Fisher's exact test), Q value = 0.023

Table S274.  Gene #52: 'del_13q14.13' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 24(13Q14.13) MUTATED 70 149 6
DEL PEAK 24(13Q14.13) WILD-TYPE 117 139 4

Figure S274.  Get High-res Image Gene #52: 'del_13q14.13' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_13q14.13' versus 'RADIATION_THERAPY'

P value = 0.00122 (Fisher's exact test), Q value = 0.0073

Table S275.  Gene #52: 'del_13q14.13' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 24(13Q14.13) MUTATED 169 39
DEL PEAK 24(13Q14.13) WILD-TYPE 221 20

Figure S275.  Get High-res Image Gene #52: 'del_13q14.13' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_13q14.13' versus 'RESIDUAL_TUMOR'

P value = 0.00224 (Fisher's exact test), Q value = 0.011

Table S276.  Gene #52: 'del_13q14.13' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 24(13Q14.13) MUTATED 126 82 1 9
DEL PEAK 24(13Q14.13) WILD-TYPE 187 62 4 6

Figure S276.  Get High-res Image Gene #52: 'del_13q14.13' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_13q14.13' versus 'GLEASON_SCORE'

P value = 1.97e-05 (Wilcoxon-test), Q value = 0.00028

Table S277.  Gene #52: 'del_13q14.13' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 24(13Q14.13) MUTATED 227 7.8 (1.0)
DEL PEAK 24(13Q14.13) WILD-TYPE 265 7.4 (1.0)

Figure S277.  Get High-res Image Gene #52: 'del_13q14.13' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_13q14.13' versus 'RACE'

P value = 0.00409 (Fisher's exact test), Q value = 0.018

Table S278.  Gene #52: 'del_13q14.13' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 7 146
DEL PEAK 24(13Q14.13) MUTATED 1 7 64
DEL PEAK 24(13Q14.13) WILD-TYPE 1 0 82

Figure S278.  Get High-res Image Gene #52: 'del_13q14.13' versus Clinical Feature #11: 'RACE'

'del_13q22.1' versus 'YEARS_TO_BIRTH'

P value = 0.000926 (Wilcoxon-test), Q value = 0.0057

Table S279.  Gene #53: 'del_13q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
DEL PEAK 25(13Q22.1) MUTATED 173 62.3 (6.7)
DEL PEAK 25(13Q22.1) WILD-TYPE 308 60.3 (6.8)

Figure S279.  Get High-res Image Gene #53: 'del_13q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q22.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00021 (Fisher's exact test), Q value = 0.002

Table S280.  Gene #53: 'del_13q22.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 25(13Q22.1) MUTATED 50 116 8
DEL PEAK 25(13Q22.1) WILD-TYPE 137 172 2

Figure S280.  Get High-res Image Gene #53: 'del_13q22.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_13q22.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0921 (Fisher's exact test), Q value = 0.2

Table S281.  Gene #53: 'del_13q22.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 25(13Q22.1) MUTATED 124 36
DEL PEAK 25(13Q22.1) WILD-TYPE 219 41

Figure S281.  Get High-res Image Gene #53: 'del_13q22.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_13q22.1' versus 'RADIATION_THERAPY'

P value = 0.112 (Fisher's exact test), Q value = 0.24

Table S282.  Gene #53: 'del_13q22.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 25(13Q22.1) MUTATED 136 27
DEL PEAK 25(13Q22.1) WILD-TYPE 254 32

Figure S282.  Get High-res Image Gene #53: 'del_13q22.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_13q22.1' versus 'RESIDUAL_TUMOR'

P value = 0.0132 (Fisher's exact test), Q value = 0.047

Table S283.  Gene #53: 'del_13q22.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 25(13Q22.1) MUTATED 96 65 1 7
DEL PEAK 25(13Q22.1) WILD-TYPE 217 79 4 8

Figure S283.  Get High-res Image Gene #53: 'del_13q22.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_13q22.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0445 (Wilcoxon-test), Q value = 0.12

Table S284.  Gene #53: 'del_13q22.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 25(13Q22.1) MUTATED 151 0.6 (1.6)
DEL PEAK 25(13Q22.1) WILD-TYPE 251 0.3 (1.2)

Figure S284.  Get High-res Image Gene #53: 'del_13q22.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_13q22.1' versus 'GLEASON_SCORE'

P value = 3.04e-10 (Wilcoxon-test), Q value = 3.5e-08

Table S285.  Gene #53: 'del_13q22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 25(13Q22.1) MUTATED 176 8.0 (1.0)
DEL PEAK 25(13Q22.1) WILD-TYPE 316 7.4 (1.0)

Figure S285.  Get High-res Image Gene #53: 'del_13q22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_13q22.1' versus 'RACE'

P value = 4e-04 (Fisher's exact test), Q value = 0.0031

Table S286.  Gene #53: 'del_13q22.1' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 7 146
DEL PEAK 25(13Q22.1) MUTATED 0 7 51
DEL PEAK 25(13Q22.1) WILD-TYPE 2 0 95

Figure S286.  Get High-res Image Gene #53: 'del_13q22.1' versus Clinical Feature #11: 'RACE'

'del_15q21.3' versus 'PATHOLOGY_T_STAGE'

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

Table S287.  Gene #54: 'del_15q21.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 26(15Q21.3) MUTATED 9 54 4
DEL PEAK 26(15Q21.3) WILD-TYPE 178 234 6

Figure S287.  Get High-res Image Gene #54: 'del_15q21.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_15q21.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00178 (Fisher's exact test), Q value = 0.0096

Table S288.  Gene #54: 'del_15q21.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 26(15Q21.3) MUTATED 39 20
DEL PEAK 26(15Q21.3) WILD-TYPE 304 57

Figure S288.  Get High-res Image Gene #54: 'del_15q21.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_15q21.3' versus 'RADIATION_THERAPY'

P value = 0.0067 (Fisher's exact test), Q value = 0.027

Table S289.  Gene #54: 'del_15q21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 26(15Q21.3) MUTATED 45 15
DEL PEAK 26(15Q21.3) WILD-TYPE 345 44

Figure S289.  Get High-res Image Gene #54: 'del_15q21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_15q21.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000302 (Wilcoxon-test), Q value = 0.0026

Table S290.  Gene #54: 'del_15q21.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 26(15Q21.3) MUTATED 58 0.8 (1.4)
DEL PEAK 26(15Q21.3) WILD-TYPE 344 0.4 (1.3)

Figure S290.  Get High-res Image Gene #54: 'del_15q21.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_15q21.3' versus 'GLEASON_SCORE'

P value = 8.97e-09 (Wilcoxon-test), Q value = 4.8e-07

Table S291.  Gene #54: 'del_15q21.3' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 26(15Q21.3) MUTATED 67 8.3 (1.0)
DEL PEAK 26(15Q21.3) WILD-TYPE 425 7.5 (1.0)

Figure S291.  Get High-res Image Gene #54: 'del_15q21.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_15q21.3' versus 'PSA_VALUE'

P value = 0.121 (Wilcoxon-test), Q value = 0.25

Table S292.  Gene #54: 'del_15q21.3' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
DEL PEAK 26(15Q21.3) MUTATED 53 1.9 (5.9)
DEL PEAK 26(15Q21.3) WILD-TYPE 382 1.7 (16.9)

Figure S292.  Get High-res Image Gene #54: 'del_15q21.3' versus Clinical Feature #10: 'PSA_VALUE'

'del_16q22.3' versus 'YEARS_TO_BIRTH'

P value = 0.039 (Wilcoxon-test), Q value = 0.11

Table S293.  Gene #55: 'del_16q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
DEL PEAK 27(16Q22.3) MUTATED 187 61.8 (6.6)
DEL PEAK 27(16Q22.3) WILD-TYPE 294 60.5 (6.9)

Figure S293.  Get High-res Image Gene #55: 'del_16q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q22.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00033 (Fisher's exact test), Q value = 0.0027

Table S294.  Gene #55: 'del_16q22.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 27(16Q22.3) MUTATED 53 130 6
DEL PEAK 27(16Q22.3) WILD-TYPE 134 158 4

Figure S294.  Get High-res Image Gene #55: 'del_16q22.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_16q22.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0294 (Fisher's exact test), Q value = 0.087

Table S295.  Gene #55: 'del_16q22.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 27(16Q22.3) MUTATED 131 40
DEL PEAK 27(16Q22.3) WILD-TYPE 212 37

Figure S295.  Get High-res Image Gene #55: 'del_16q22.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_16q22.3' versus 'RESIDUAL_TUMOR'

P value = 0.0284 (Fisher's exact test), Q value = 0.086

Table S296.  Gene #55: 'del_16q22.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 27(16Q22.3) MUTATED 109 70 1 5
DEL PEAK 27(16Q22.3) WILD-TYPE 204 74 4 10

Figure S296.  Get High-res Image Gene #55: 'del_16q22.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_16q22.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00793 (Wilcoxon-test), Q value = 0.031

Table S297.  Gene #55: 'del_16q22.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 27(16Q22.3) MUTATED 162 0.6 (1.7)
DEL PEAK 27(16Q22.3) WILD-TYPE 240 0.3 (1.0)

Figure S297.  Get High-res Image Gene #55: 'del_16q22.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_16q22.3' versus 'GLEASON_SCORE'

P value = 4.97e-09 (Wilcoxon-test), Q value = 3.1e-07

Table S298.  Gene #55: 'del_16q22.3' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 27(16Q22.3) MUTATED 191 7.9 (1.0)
DEL PEAK 27(16Q22.3) WILD-TYPE 301 7.4 (1.0)

Figure S298.  Get High-res Image Gene #55: 'del_16q22.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_16q22.3' versus 'PSA_VALUE'

P value = 0.114 (Wilcoxon-test), Q value = 0.24

Table S299.  Gene #55: 'del_16q22.3' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
DEL PEAK 27(16Q22.3) MUTATED 164 1.4 (4.7)
DEL PEAK 27(16Q22.3) WILD-TYPE 271 2.0 (19.9)

Figure S299.  Get High-res Image Gene #55: 'del_16q22.3' versus Clinical Feature #10: 'PSA_VALUE'

'del_16q24.1' versus 'PATHOLOGY_T_STAGE'

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

Table S300.  Gene #56: 'del_16q24.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 28(16Q24.1) MUTATED 56 148 6
DEL PEAK 28(16Q24.1) WILD-TYPE 131 140 4

Figure S300.  Get High-res Image Gene #56: 'del_16q24.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_16q24.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.043 (Fisher's exact test), Q value = 0.12

Table S301.  Gene #56: 'del_16q24.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 28(16Q24.1) MUTATED 147 43
DEL PEAK 28(16Q24.1) WILD-TYPE 196 34

Figure S301.  Get High-res Image Gene #56: 'del_16q24.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_16q24.1' versus 'RESIDUAL_TUMOR'

P value = 0.109 (Fisher's exact test), Q value = 0.23

Table S302.  Gene #56: 'del_16q24.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 28(16Q24.1) MUTATED 125 74 2 5
DEL PEAK 28(16Q24.1) WILD-TYPE 188 70 3 10

Figure S302.  Get High-res Image Gene #56: 'del_16q24.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_16q24.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0164 (Wilcoxon-test), Q value = 0.056

Table S303.  Gene #56: 'del_16q24.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 28(16Q24.1) MUTATED 182 0.6 (1.8)
DEL PEAK 28(16Q24.1) WILD-TYPE 220 0.3 (0.8)

Figure S303.  Get High-res Image Gene #56: 'del_16q24.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_16q24.1' versus 'GLEASON_SCORE'

P value = 2.12e-09 (Wilcoxon-test), Q value = 1.5e-07

Table S304.  Gene #56: 'del_16q24.1' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 28(16Q24.1) MUTATED 213 7.9 (1.0)
DEL PEAK 28(16Q24.1) WILD-TYPE 279 7.4 (0.9)

Figure S304.  Get High-res Image Gene #56: 'del_16q24.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_16q24.1' versus 'PSA_VALUE'

P value = 0.0798 (Wilcoxon-test), Q value = 0.18

Table S305.  Gene #56: 'del_16q24.1' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
DEL PEAK 28(16Q24.1) MUTATED 185 3.3 (24.2)
DEL PEAK 28(16Q24.1) WILD-TYPE 250 0.6 (3.0)

Figure S305.  Get High-res Image Gene #56: 'del_16q24.1' versus Clinical Feature #10: 'PSA_VALUE'

'del_17p13.1' versus 'PATHOLOGY_T_STAGE'

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

Table S306.  Gene #57: 'del_17p13.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 29(17P13.1) MUTATED 39 115 6
DEL PEAK 29(17P13.1) WILD-TYPE 148 173 4

Figure S306.  Get High-res Image Gene #57: 'del_17p13.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_17p13.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00359 (Fisher's exact test), Q value = 0.017

Table S307.  Gene #57: 'del_17p13.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 29(17P13.1) MUTATED 108 38
DEL PEAK 29(17P13.1) WILD-TYPE 235 39

Figure S307.  Get High-res Image Gene #57: 'del_17p13.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_17p13.1' versus 'RADIATION_THERAPY'

P value = 0.0176 (Fisher's exact test), Q value = 0.06

Table S308.  Gene #57: 'del_17p13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 29(17P13.1) MUTATED 122 28
DEL PEAK 29(17P13.1) WILD-TYPE 268 31

Figure S308.  Get High-res Image Gene #57: 'del_17p13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_17p13.1' versus 'RESIDUAL_TUMOR'

P value = 0.0113 (Fisher's exact test), Q value = 0.042

Table S309.  Gene #57: 'del_17p13.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 29(17P13.1) MUTATED 92 62 0 4
DEL PEAK 29(17P13.1) WILD-TYPE 221 82 5 11

Figure S309.  Get High-res Image Gene #57: 'del_17p13.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_17p13.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000285 (Wilcoxon-test), Q value = 0.0025

Table S310.  Gene #57: 'del_17p13.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 29(17P13.1) MUTATED 136 0.7 (1.7)
DEL PEAK 29(17P13.1) WILD-TYPE 266 0.3 (1.2)

Figure S310.  Get High-res Image Gene #57: 'del_17p13.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_17p13.1' versus 'GLEASON_SCORE'

P value = 1.3e-09 (Wilcoxon-test), Q value = 1e-07

Table S311.  Gene #57: 'del_17p13.1' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 29(17P13.1) MUTATED 163 8.0 (1.0)
DEL PEAK 29(17P13.1) WILD-TYPE 329 7.4 (0.9)

Figure S311.  Get High-res Image Gene #57: 'del_17p13.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_17q21.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.12 (Fisher's exact test), Q value = 0.25

Table S312.  Gene #58: 'del_17q21.31' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 30(17Q21.31) MUTATED 29 63 3
DEL PEAK 30(17Q21.31) WILD-TYPE 158 225 7

Figure S312.  Get High-res Image Gene #58: 'del_17q21.31' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_18q21.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.00046 (Fisher's exact test), Q value = 0.0034

Table S313.  Gene #59: 'del_18q21.31' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 31(18Q21.31) MUTATED 32 93 4
DEL PEAK 31(18Q21.31) WILD-TYPE 155 195 6

Figure S313.  Get High-res Image Gene #59: 'del_18q21.31' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_18q21.31' versus 'PATHOLOGY_N_STAGE'

P value = 0.0244 (Fisher's exact test), Q value = 0.077

Table S314.  Gene #59: 'del_18q21.31' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 31(18Q21.31) MUTATED 88 30
DEL PEAK 31(18Q21.31) WILD-TYPE 255 47

Figure S314.  Get High-res Image Gene #59: 'del_18q21.31' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_18q21.31' versus 'RADIATION_THERAPY'

P value = 0.111 (Fisher's exact test), Q value = 0.24

Table S315.  Gene #59: 'del_18q21.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 31(18Q21.31) MUTATED 97 21
DEL PEAK 31(18Q21.31) WILD-TYPE 293 38

Figure S315.  Get High-res Image Gene #59: 'del_18q21.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_18q21.31' versus 'RESIDUAL_TUMOR'

P value = 0.00069 (Fisher's exact test), Q value = 0.0046

Table S316.  Gene #59: 'del_18q21.31' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 31(18Q21.31) MUTATED 70 56 0 2
DEL PEAK 31(18Q21.31) WILD-TYPE 243 88 5 13

Figure S316.  Get High-res Image Gene #59: 'del_18q21.31' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_18q21.31' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00979 (Wilcoxon-test), Q value = 0.038

Table S317.  Gene #59: 'del_18q21.31' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 31(18Q21.31) MUTATED 113 0.7 (2.0)
DEL PEAK 31(18Q21.31) WILD-TYPE 289 0.3 (1.0)

Figure S317.  Get High-res Image Gene #59: 'del_18q21.31' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_18q21.31' versus 'GLEASON_SCORE'

P value = 3.15e-06 (Wilcoxon-test), Q value = 8.1e-05

Table S318.  Gene #59: 'del_18q21.31' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 31(18Q21.31) MUTATED 131 8.0 (1.0)
DEL PEAK 31(18Q21.31) WILD-TYPE 361 7.5 (1.0)

Figure S318.  Get High-res Image Gene #59: 'del_18q21.31' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_18q23' versus 'PATHOLOGY_T_STAGE'

P value = 0.00051 (Fisher's exact test), Q value = 0.0035

Table S319.  Gene #60: 'del_18q23' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 32(18Q23) MUTATED 34 97 4
DEL PEAK 32(18Q23) WILD-TYPE 153 191 6

Figure S319.  Get High-res Image Gene #60: 'del_18q23' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_18q23' versus 'PATHOLOGY_N_STAGE'

P value = 0.00537 (Fisher's exact test), Q value = 0.023

Table S320.  Gene #60: 'del_18q23' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 32(18Q23) MUTATED 90 33
DEL PEAK 32(18Q23) WILD-TYPE 253 44

Figure S320.  Get High-res Image Gene #60: 'del_18q23' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_18q23' versus 'RESIDUAL_TUMOR'

P value = 0.00263 (Fisher's exact test), Q value = 0.013

Table S321.  Gene #60: 'del_18q23' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 32(18Q23) MUTATED 75 56 0 2
DEL PEAK 32(18Q23) WILD-TYPE 238 88 5 13

Figure S321.  Get High-res Image Gene #60: 'del_18q23' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_18q23' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00154 (Wilcoxon-test), Q value = 0.0088

Table S322.  Gene #60: 'del_18q23' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 32(18Q23) MUTATED 118 0.8 (2.1)
DEL PEAK 32(18Q23) WILD-TYPE 284 0.3 (0.9)

Figure S322.  Get High-res Image Gene #60: 'del_18q23' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_18q23' versus 'GLEASON_SCORE'

P value = 6.47e-07 (Wilcoxon-test), Q value = 2.1e-05

Table S323.  Gene #60: 'del_18q23' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 32(18Q23) MUTATED 137 8.0 (1.0)
DEL PEAK 32(18Q23) WILD-TYPE 355 7.5 (1.0)

Figure S323.  Get High-res Image Gene #60: 'del_18q23' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_18q23' versus 'PSA_VALUE'

P value = 0.0306 (Wilcoxon-test), Q value = 0.089

Table S324.  Gene #60: 'del_18q23' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
DEL PEAK 32(18Q23) MUTATED 121 4.3 (29.7)
DEL PEAK 32(18Q23) WILD-TYPE 314 0.8 (3.3)

Figure S324.  Get High-res Image Gene #60: 'del_18q23' versus Clinical Feature #10: 'PSA_VALUE'

'del_19q13.2' versus 'Time to Death'

P value = 0.11 (logrank test), Q value = 0.23

Table S325.  Gene #61: 'del_19q13.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 492 9 0.8 - 165.2 (30.6)
DEL PEAK 33(19Q13.2) MUTATED 52 2 0.8 - 113.3 (30.1)
DEL PEAK 33(19Q13.2) WILD-TYPE 440 7 0.9 - 165.2 (30.8)

Figure S325.  Get High-res Image Gene #61: 'del_19q13.2' versus Clinical Feature #1: 'Time to Death'

'del_19q13.2' versus 'YEARS_TO_BIRTH'

P value = 0.0505 (Wilcoxon-test), Q value = 0.13

Table S326.  Gene #61: 'del_19q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
DEL PEAK 33(19Q13.2) MUTATED 51 62.6 (6.6)
DEL PEAK 33(19Q13.2) WILD-TYPE 430 60.8 (6.8)

Figure S326.  Get High-res Image Gene #61: 'del_19q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19q13.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00696 (Fisher's exact test), Q value = 0.028

Table S327.  Gene #61: 'del_19q13.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 33(19Q13.2) MUTATED 11 37 3
DEL PEAK 33(19Q13.2) WILD-TYPE 176 251 7

Figure S327.  Get High-res Image Gene #61: 'del_19q13.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_19q13.2' versus 'RESIDUAL_TUMOR'

P value = 0.0435 (Fisher's exact test), Q value = 0.12

Table S328.  Gene #61: 'del_19q13.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
DEL PEAK 33(19Q13.2) MUTATED 27 24 0 0
DEL PEAK 33(19Q13.2) WILD-TYPE 286 120 5 15

Figure S328.  Get High-res Image Gene #61: 'del_19q13.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_19q13.2' versus 'GLEASON_SCORE'

P value = 0.000273 (Wilcoxon-test), Q value = 0.0025

Table S329.  Gene #61: 'del_19q13.2' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 33(19Q13.2) MUTATED 52 8.1 (1.0)
DEL PEAK 33(19Q13.2) WILD-TYPE 440 7.5 (1.0)

Figure S329.  Get High-res Image Gene #61: 'del_19q13.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_21q22.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00181 (Fisher's exact test), Q value = 0.0096

Table S330.  Gene #62: 'del_21q22.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 34(21Q22.2) MUTATED 10 39 3
DEL PEAK 34(21Q22.2) WILD-TYPE 177 249 7

Figure S330.  Get High-res Image Gene #62: 'del_21q22.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_21q22.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0655 (Fisher's exact test), Q value = 0.16

Table S331.  Gene #62: 'del_21q22.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
DEL PEAK 34(21Q22.2) MUTATED 32 13
DEL PEAK 34(21Q22.2) WILD-TYPE 311 64

Figure S331.  Get High-res Image Gene #62: 'del_21q22.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_21q22.2' versus 'RADIATION_THERAPY'

P value = 0.0691 (Fisher's exact test), Q value = 0.17

Table S332.  Gene #62: 'del_21q22.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
DEL PEAK 34(21Q22.2) MUTATED 38 11
DEL PEAK 34(21Q22.2) WILD-TYPE 352 48

Figure S332.  Get High-res Image Gene #62: 'del_21q22.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_21q22.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0373 (Wilcoxon-test), Q value = 0.1

Table S333.  Gene #62: 'del_21q22.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 34(21Q22.2) MUTATED 42 0.8 (1.9)
DEL PEAK 34(21Q22.2) WILD-TYPE 360 0.4 (1.3)

Figure S333.  Get High-res Image Gene #62: 'del_21q22.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_21q22.2' versus 'GLEASON_SCORE'

P value = 0.0367 (Wilcoxon-test), Q value = 0.1

Table S334.  Gene #62: 'del_21q22.2' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
DEL PEAK 34(21Q22.2) MUTATED 52 7.9 (1.1)
DEL PEAK 34(21Q22.2) WILD-TYPE 440 7.6 (1.0)

Figure S334.  Get High-res Image Gene #62: 'del_21q22.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_21q22.2' versus 'RACE'

P value = 0.0763 (Fisher's exact test), Q value = 0.17

Table S335.  Gene #62: 'del_21q22.2' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 7 146
DEL PEAK 34(21Q22.2) MUTATED 1 2 15
DEL PEAK 34(21Q22.2) WILD-TYPE 1 5 131

Figure S335.  Get High-res Image Gene #62: 'del_21q22.2' versus Clinical Feature #11: 'RACE'

'del_21q22.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0561 (Fisher's exact test), Q value = 0.14

Table S336.  Gene #63: 'del_21q22.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
DEL PEAK 35(21Q22.3) MUTATED 46 94 5
DEL PEAK 35(21Q22.3) WILD-TYPE 141 194 5

Figure S336.  Get High-res Image Gene #63: 'del_21q22.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_21q22.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0367 (Wilcoxon-test), Q value = 0.1

Table S337.  Gene #63: 'del_21q22.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
DEL PEAK 35(21Q22.3) MUTATED 119 0.7 (2.0)
DEL PEAK 35(21Q22.3) WILD-TYPE 283 0.3 (1.0)

Figure S337.  Get High-res Image Gene #63: 'del_21q22.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/22533739/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PRAD-TP/22506989/PRAD-TP.merged_data.txt

  • Number of patients = 492

  • Number of significantly focal cnvs = 63

  • Number of selected clinical features = 11

  • Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' 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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[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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