Correlation between copy number variation genes (focal events) and selected clinical features

Prostate Adenocarcinoma (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1W37VKS

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 65 focal events and 11 clinical features across 491 patients, 351 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', 'RADIATION_THERAPY', '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', 'RADIATION_THERAPY', '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', and 'GLEASON_SCORE'.
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_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_19q13.43 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', '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_xp22.11 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_xp22.11 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', 'GLEASON_SCORE', and 'PSA_VALUE'.
amp_xp21.1 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', 'GLEASON_SCORE', 'PSA_VALUE', and 'RACE'.
amp_xq21.1 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 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_xq25 cnv correlated to 'PATHOLOGY_T_STAGE', 'GLEASON_SCORE', and 'RACE'.
amp_xq27.1 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'GLEASON_SCORE', and 'PSA_VALUE'.
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_7q31.33 cnv correlated to 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
del_8p23.2 cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', 'GLEASON_SCORE', and 'PSA_VALUE'.
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', 'RADIATION_THERAPY', '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 65 focal events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 351 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 xp21 1	23 (5%)	468	0.543 (0.697)	0.00157 (0.00943)	0.00542 (0.0238)	0.0499 (0.132)	0.736 (0.865)	0.0233 (0.0752)	0.0175 (0.0618)	0.0463 (0.124)	0.000232 (0.00224)	0.113 (0.235)	0.00745 (0.0317)
amp 1q22	39 (8%)	452	0.417 (0.588)	0.0122 (0.0463)	1e-05 (0.000162)	0.000557 (0.00419)	0.033 (0.0952)	0.0191 (0.0653)	0.0534 (0.137)	0.000171 (0.00183)	3.24e-07 (1.16e-05)	0.163 (0.315)	1 (1.00)
amp 3q26 2	85 (17%)	406	0.29 (0.476)	0.0247 (0.0784)	1e-05 (0.000162)	0.000636 (0.00459)	0.0871 (0.194)	0.278 (0.465)	0.0003 (0.00268)	5.74e-05 (0.000747)	2.17e-09 (1.72e-07)	0.0511 (0.133)	1 (1.00)
amp 8q22 1	156 (32%)	335	0.56 (0.707)	0.0909 (0.201)	1e-05 (0.000162)	0.00142 (0.00873)	0.00877 (0.036)	0.564 (0.708)	2e-05 (0.000292)	0.000483 (0.00383)	2.43e-13 (1.74e-10)	0.0606 (0.148)	1 (1.00)
amp 8q24 21	151 (31%)	340	0.973 (1.00)	0.057 (0.143)	1e-05 (0.000162)	0.000738 (0.00517)	0.0304 (0.0889)	0.566 (0.708)	0.00024 (0.00229)	0.000147 (0.0016)	1.53e-12 (3.64e-10)	0.0321 (0.0937)	0.812 (0.92)
amp 15q11 2	15 (3%)	476	0.0932 (0.203)	0.085 (0.19)	0.118 (0.242)	0.000143 (0.00157)	0.0586 (0.146)	1 (1.00)	0.0344 (0.0975)	4.27e-06 (0.000122)	0.00307 (0.0156)	0.628 (0.765)
amp 16q11 2	30 (6%)	461	0.507 (0.666)	0.0262 (0.0816)	0.00029 (0.00266)	0.0728 (0.169)	0.0539 (0.137)	0.208 (0.38)	0.038 (0.105)	0.0589 (0.146)	1.57e-06 (4.88e-05)	0.0205 (0.0691)	1 (1.00)
amp 17q23 2	25 (5%)	466	0.12 (0.243)	0.171 (0.328)	0.00084 (0.00567)	0.0217 (0.071)	0.0539 (0.137)	0.0293 (0.0868)	0.203 (0.373)	0.0111 (0.0433)	7.09e-05 (0.000874)	0.0497 (0.132)	1 (1.00)
amp 20q13 2	44 (9%)	447	0.969 (1.00)	0.00493 (0.0224)	2e-05 (0.000292)	0.00857 (0.0354)	0.0767 (0.177)	0.362 (0.55)	0.0206 (0.0691)	0.00343 (0.0168)	1.51e-07 (6.36e-06)	0.0647 (0.155)	1 (1.00)
amp xp22 11	25 (5%)	466	0.592 (0.733)	0.0135 (0.0501)	0.00236 (0.013)	0.104 (0.221)	0.0436 (0.118)	0.0293 (0.0868)	0.0179 (0.0626)	0.0862 (0.192)	0.000988 (0.00654)	0.314 (0.5)	0.259 (0.444)
amp xp22 11	24 (5%)	467	0.552 (0.702)	0.0782 (0.178)	0.00217 (0.0122)	0.06 (0.147)	0.502 (0.661)	0.0262 (0.0816)	0.0177 (0.0625)	0.0642 (0.154)	0.00115 (0.0074)	0.0996 (0.213)	0.215 (0.389)
del 13q22 1	176 (36%)	315	0.298 (0.483)	0.000883 (0.0059)	0.00011 (0.00125)	0.0927 (0.202)	0.0773 (0.177)	0.397 (0.575)	0.0129 (0.0484)	0.037 (0.103)	2.15e-10 (3.08e-08)	0.291 (0.476)	0.00047 (0.00378)
amp 3q21 3	74 (15%)	417	0.209 (0.38)	0.00282 (0.0148)	1e-05 (0.000162)	0.0012 (0.0075)	0.0265 (0.0816)	0.244 (0.423)	0.00044 (0.00366)	0.000105 (0.00121)	7.01e-11 (1.25e-08)	0.136 (0.272)	0.659 (0.793)
amp 9q33 3	61 (12%)	430	0.912 (1.00)	0.0274 (0.0838)	1e-05 (0.000162)	1.2e-08 (6.57e-07)	0.187 (0.351)	0.0828 (0.187)	0.00078 (0.00531)	2.74e-10 (3.26e-08)	1.3e-12 (3.64e-10)	0.229 (0.408)	0.555 (0.703)
amp 11q13 2	47 (10%)	444	0.407 (0.585)	0.000569 (0.00423)	1e-05 (0.000162)	6.26e-06 (0.000162)	0.0963 (0.207)	0.634 (0.77)	0.00303 (0.0155)	2.87e-07 (1.08e-05)	2.28e-08 (1.09e-06)	0.579 (0.721)	0.345 (0.533)
amp 12q23 1	36 (7%)	455	0.387 (0.567)	0.116 (0.238)	0.0007 (0.005)	0.000204 (0.00204)	0.012 (0.0457)	1 (1.00)	0.0003 (0.00268)	2.77e-05 (0.000389)	9.96e-07 (3.24e-05)	0.374 (0.562)	1 (1.00)
amp xq21 1	14 (3%)	477	0.597 (0.736)	0.0164 (0.0584)	0.0198 (0.0675)	0.0277 (0.0842)	0.683 (0.815)	1 (1.00)	0.0798 (0.181)	0.0253 (0.0801)	0.00207 (0.0118)	0.375 (0.562)	0.0273 (0.0837)
del 5q11 2	99 (20%)	392	0.656 (0.791)	0.0257 (0.081)	1e-05 (0.000162)	0.000371 (0.00323)	0.00766 (0.0322)	0.746 (0.869)	0.0283 (0.0857)	1.49e-05 (0.000232)	5.05e-10 (5.16e-08)	0.406 (0.584)	0.438 (0.609)
del 16q22 3	190 (39%)	301	0.435 (0.607)	0.0415 (0.115)	0.00022 (0.00215)	0.0289 (0.0868)	0.563 (0.708)	1 (1.00)	0.0324 (0.0941)	0.0106 (0.0423)	7.22e-09 (4.69e-07)	0.0905 (0.2)	0.718 (0.848)
del 18q23	136 (28%)	355	0.467 (0.633)	0.148 (0.293)	0.0005 (0.00384)	0.00519 (0.023)	0.11 (0.231)	1 (1.00)	0.0037 (0.0178)	0.00234 (0.013)	9.81e-07 (3.24e-05)	0.033 (0.0952)	0.446 (0.618)
amp 4q13 3	22 (4%)	469	0.53 (0.688)	0.019 (0.0653)	0.00184 (0.0107)	0.000521 (0.00397)	0.294 (0.479)	0.478 (0.643)	0.00507 (0.0227)	5.14e-05 (0.000681)	0.000256 (0.00238)	0.378 (0.562)	1 (1.00)
amp 5q35 3	28 (6%)	463	0.449 (0.62)	2.6e-07 (1.03e-05)	0.00019 (0.00197)	0.000717 (0.00508)	0.556 (0.703)	0.565 (0.708)	0.0621 (0.151)	6.35e-05 (0.000811)	3.64e-05 (0.000501)	0.931 (1.00)	0.264 (0.45)
amp 14q21 1	30 (6%)	461	0.682 (0.815)	0.0368 (0.103)	0.0691 (0.163)	0.0148 (0.0538)	0.00319 (0.016)	0.208 (0.38)	0.415 (0.588)	0.0055 (0.0239)	7.74e-05 (0.000938)	0.915 (1.00)	1 (1.00)
amp 19q13 43	18 (4%)	473	0.24 (0.419)	0.0301 (0.0885)	0.0005 (0.00384)	0.022 (0.0716)	1 (1.00)	0.089 (0.198)	0.275 (0.463)	0.0115 (0.0445)	8.97e-06 (0.000162)	0.447 (0.618)	1 (1.00)
del 6q14 3	179 (36%)	312	0.342 (0.531)	0.00104 (0.00683)	0.0666 (0.159)	0.0265 (0.0816)	0.141 (0.279)	1 (1.00)	0.00044 (0.00366)	0.018 (0.0626)	0.000445 (0.00366)	0.529 (0.688)	0.58 (0.722)
del 8p21 3	293 (60%)	198	0.389 (0.569)	0.386 (0.567)	1e-05 (0.000162)	0.00272 (0.0144)	0.0589 (0.146)	0.582 (0.722)	0.156 (0.304)	0.0013 (0.00809)	0.00109 (0.00707)	0.0838 (0.188)	0.729 (0.861)
del 10q23 31	156 (32%)	335	0.909 (1.00)	0.548 (0.701)	1e-05 (0.000162)	0.00236 (0.013)	0.0214 (0.0706)	0.774 (0.893)	0.164 (0.318)	0.00118 (0.0075)	5.3e-08 (2.37e-06)	0.00956 (0.0386)	0.235 (0.413)
del 11q22 3	43 (9%)	448	0.384 (0.566)	0.0338 (0.0966)	0.00062 (0.00452)	0.173 (0.33)	0.0529 (0.137)	0.351 (0.539)	0.00393 (0.0187)	0.068 (0.161)	6.89e-05 (0.000864)	0.806 (0.919)	0.633 (0.77)
del 12p13 1	124 (25%)	367	0.803 (0.918)	0.786 (0.902)	1e-05 (0.000162)	0.011 (0.0431)	0.0225 (0.0729)	0.129 (0.26)	0.341 (0.53)	0.00297 (0.0154)	4.49e-05 (0.000606)	0.021 (0.0699)	1 (1.00)
del 13q14 13	227 (46%)	264	0.907 (1.00)	0.0129 (0.0485)	0.00433 (0.0201)	0.209 (0.38)	0.00411 (0.0193)	0.277 (0.464)	0.00198 (0.0113)	0.178 (0.338)	1.48e-05 (0.000232)	0.319 (0.504)	0.00414 (0.0193)
del 15q21 3	66 (13%)	425	0.565 (0.708)	0.299 (0.483)	1e-05 (0.000162)	0.00155 (0.00943)	0.00261 (0.0142)	0.416 (0.588)	0.19 (0.353)	0.000614 (0.00452)	1.73e-08 (8.82e-07)	0.112 (0.235)	1 (1.00)
del 16q24 1	212 (43%)	279	0.432 (0.605)	0.251 (0.433)	2e-05 (0.000292)	0.0425 (0.117)	0.477 (0.643)	1 (1.00)	0.119 (0.243)	0.0209 (0.0699)	3.01e-09 (2.15e-07)	0.0634 (0.153)	1 (1.00)
del 17p13 1	162 (33%)	329	0.546 (0.699)	0.414 (0.588)	1e-05 (0.000162)	0.00344 (0.0168)	0.0161 (0.058)	0.781 (0.899)	0.0152 (0.0549)	0.000435 (0.00366)	1.99e-09 (1.72e-07)	0.238 (0.418)	0.823 (0.929)
del 18q21 31	130 (26%)	361	0.421 (0.592)	0.765 (0.886)	0.00045 (0.00366)	0.0239 (0.0762)	0.0505 (0.133)	1 (1.00)	0.00116 (0.00741)	0.0142 (0.0523)	4.75e-06 (0.000131)	0.253 (0.436)	0.395 (0.573)
del 21q22 2	52 (11%)	439	0.295 (0.479)	0.221 (0.397)	0.00166 (0.00981)	0.066 (0.158)	0.101 (0.216)	0.177 (0.336)	0.754 (0.875)	0.0341 (0.0972)	0.0347 (0.0981)	0.572 (0.714)	0.0774 (0.177)
amp 13q12 11	25 (5%)	466	0.79 (0.905)	0.000412 (0.00355)	0.0045 (0.0208)	0.151 (0.295)	0.338 (0.528)	0.0293 (0.0868)	0.202 (0.373)	0.0836 (0.188)	0.0107 (0.0423)	0.462 (0.632)	0.307 (0.491)
del 1p31 3	59 (12%)	432	0.476 (0.643)	0.233 (0.412)	0.00955 (0.0386)	0.128 (0.259)	0.0294 (0.0868)	0.393 (0.571)	0.0701 (0.164)	0.0989 (0.212)	0.000205 (0.00204)	0.275 (0.463)	0.199 (0.367)
del 1q42 3	47 (10%)	444	0.000102 (0.0012)	0.115 (0.236)	0.353 (0.54)	0.307 (0.491)	1 (1.00)	1 (1.00)	0.0104 (0.0419)	0.138 (0.276)	0.0679 (0.161)	0.0926 (0.202)	0.555 (0.703)
del 2p21	45 (9%)	446	0.988 (1.00)	0.15 (0.295)	0.00035 (0.00309)	0.0585 (0.146)	0.458 (0.63)	0.628 (0.765)	0.0506 (0.133)	0.0554 (0.141)	0.003 (0.0154)	0.231 (0.409)	1 (1.00)
del 5q13 2	98 (20%)	393	0.483 (0.643)	0.392 (0.571)	1e-05 (0.000162)	0.0214 (0.0706)	0.0338 (0.0966)	0.746 (0.869)	0.238 (0.418)	0.00266 (0.0142)	1.03e-08 (6.17e-07)	0.288 (0.476)	0.293 (0.479)
del 6p25 1	46 (9%)	445	0.171 (0.328)	0.32 (0.504)	0.0095 (0.0386)	0.00605 (0.0261)	0.222 (0.398)	1 (1.00)	0.617 (0.757)	0.00157 (0.00943)	8.2e-06 (0.000162)	0.487 (0.645)	0.00664 (0.0284)
del 8p23 2	223 (45%)	268	0.4 (0.578)	0.376 (0.562)	1e-05 (0.000162)	0.0112 (0.0434)	0.156 (0.304)	1 (1.00)	0.532 (0.689)	0.00532 (0.0235)	0.00459 (0.0211)	0.0689 (0.162)	0.375 (0.562)
del 9p23	45 (9%)	446	0.283 (0.47)	0.498 (0.656)	0.0238 (0.0762)	0.0201 (0.0682)	0.0963 (0.207)	1 (1.00)	0.416 (0.588)	0.00755 (0.0319)	0.00401 (0.019)	0.271 (0.46)	1 (1.00)
del 11q23 2	48 (10%)	443	0.371 (0.56)	0.0711 (0.166)	0.00264 (0.0142)	0.672 (0.806)	0.0725 (0.169)	1 (1.00)	0.0143 (0.0526)	0.808 (0.92)	8.42e-05 (0.001)	0.463 (0.632)	0.662 (0.795)
del 19q13 2	52 (11%)	439	0.109 (0.231)	0.0496 (0.132)	0.00499 (0.0224)	0.242 (0.421)	0.651 (0.786)	1 (1.00)	0.0428 (0.117)	0.239 (0.418)	0.00025 (0.00235)	0.481 (0.643)	1 (1.00)
amp 7p14 3	103 (21%)	388	0.464 (0.632)	0.0107 (0.0423)	0.0183 (0.0637)	0.358 (0.545)	0.385 (0.566)	0.744 (0.869)	0.00172 (0.0101)	0.274 (0.462)	0.000205 (0.00204)	0.997 (1.00)	1 (1.00)
amp 7q22 1	100 (20%)	391	0.465 (0.633)	0.00818 (0.0342)	0.0632 (0.153)	0.536 (0.69)	0.38 (0.563)	1 (1.00)	0.00326 (0.0163)	0.463 (0.632)	0.000185 (0.00195)	0.598 (0.736)	1 (1.00)
amp 8p11 23	67 (14%)	424	0.196 (0.365)	0.000488 (0.00383)	0.00364 (0.0176)	0.375 (0.562)	0.409 (0.586)	0.704 (0.837)	0.0119 (0.0457)	0.268 (0.456)	1.67e-06 (4.99e-05)	0.786 (0.902)	1 (1.00)
amp xq27 1	19 (4%)	472	0.188 (0.352)	0.0216 (0.0708)	0.0774 (0.177)	0.53 (0.688)	1 (1.00)	1 (1.00)	0.171 (0.328)	0.684 (0.816)	0.0371 (0.103)	0.114 (0.236)	0.423 (0.594)
del 1p22 1	58 (12%)	433	0.949 (1.00)	0.515 (0.676)	0.00267 (0.0142)	0.128 (0.259)	0.187 (0.351)	0.39 (0.569)	0.0911 (0.201)	0.0435 (0.118)	0.000132 (0.00148)	0.976 (1.00)	1 (1.00)
del 4q28 2	50 (10%)	441	0.357 (0.544)	0.00158 (0.00943)	0.0595 (0.146)	0.54 (0.695)	0.11 (0.231)	0.644 (0.781)	0.536 (0.69)	0.378 (0.562)	0.000761 (0.00523)	0.591 (0.733)	0.299 (0.483)
del 5q21 1	108 (22%)	383	0.517 (0.676)	0.0567 (0.143)	0.0258 (0.081)	0.883 (0.992)	0.312 (0.497)	0.744 (0.869)	0.474 (0.642)	0.676 (0.81)	0.00185 (0.0107)	0.0755 (0.175)	0.734 (0.864)
del 11p11 2	34 (7%)	457	0.528 (0.688)	0.516 (0.676)	0.0164 (0.0584)	0.479 (0.643)	1 (1.00)	0.613 (0.753)	0.043 (0.117)	0.329 (0.516)	0.0121 (0.046)	0.597 (0.736)	0.00346 (0.0168)
del 12q24 32	43 (9%)	448	0.904 (1.00)	0.817 (0.924)	0.00294 (0.0153)	0.0291 (0.0868)	0.325 (0.512)	1 (1.00)	0.328 (0.516)	0.0147 (0.0536)	0.054 (0.137)	0.981 (1.00)	1 (1.00)
amp 4p16 3	19 (4%)	472	0.535 (0.69)	0.0452 (0.122)	0.00076 (0.00523)	0.346 (0.533)	0.711 (0.843)	0.429 (0.601)	0.232 (0.411)	0.344 (0.533)	0.00843 (0.035)	0.377 (0.562)	1 (1.00)
amp xq21 1	16 (3%)	475	0.551 (0.702)	0.0594 (0.146)	0.0432 (0.118)	0.188 (0.352)	1 (1.00)	1 (1.00)	0.138 (0.276)	0.221 (0.397)	0.00551 (0.0239)	0.438 (0.609)	0.348 (0.534)
amp xq25	19 (4%)	472	0.281 (0.469)	0.288 (0.476)	0.0505 (0.133)	0.346 (0.533)	1 (1.00)	1 (1.00)	0.189 (0.352)	0.403 (0.581)	0.00495 (0.0224)	0.15 (0.295)	0.0188 (0.0649)
del 7q31 33	28 (6%)	463	0.811 (0.92)	0.312 (0.497)	0.383 (0.566)	0.104 (0.221)	0.353 (0.54)	1 (1.00)	0.95 (1.00)	0.037 (0.103)	0.0924 (0.202)	0.885 (0.994)	1 (1.00)
del 2q22 1	91 (19%)	400	0.483 (0.643)	2.24e-05 (0.00032)	0.15 (0.295)	1 (1.00)	0.715 (0.846)	0.484 (0.643)	0.29 (0.476)	0.939 (1.00)	0.0135 (0.0501)	0.415 (0.588)	0.416 (0.588)
del 2q22 3	84 (17%)	407	0.416 (0.588)	0.00332 (0.0165)	0.481 (0.643)	0.619 (0.757)	0.705 (0.837)	0.482 (0.643)	0.55 (0.702)	0.495 (0.654)	0.0947 (0.205)	0.246 (0.427)	1 (1.00)
del 3p13	78 (16%)	413	0.619 (0.757)	0.0513 (0.133)	0.933 (1.00)	0.304 (0.489)	0.114 (0.236)	0.254 (0.436)	0.29 (0.476)	0.26 (0.444)	0.224 (0.401)	0.745 (0.869)	1 (1.00)
del 21q22 3	146 (30%)	345	0.278 (0.465)	0.168 (0.323)	0.0509 (0.133)	0.132 (0.266)	0.219 (0.395)	0.569 (0.711)	0.747 (0.869)	0.0572 (0.144)	0.207 (0.379)	0.45 (0.62)	0.135 (0.27)
del 3q29	32 (7%)	459	0.439 (0.609)	0.648 (0.784)	0.198 (0.367)	0.332 (0.52)	0.288 (0.476)	0.23 (0.409)	0.183 (0.346)	0.273 (0.462)	0.109 (0.231)	0.923 (1.00)	1 (1.00)
del 17q21 31	96 (20%)	395	0.461 (0.632)	0.306 (0.491)	0.114 (0.236)	0.874 (0.984)	1 (1.00)	0.742 (0.869)	0.959 (1.00)	0.86 (0.97)	0.319 (0.504)	0.946 (1.00)	0.763 (0.884)
del 1q23 1	28 (6%)	463	0.366 (0.554)	0.14 (0.278)	0.383 (0.566)	0.8 (0.915)	0.768 (0.887)	1 (1.00)	0.486 (0.645)	0.811 (0.92)	0.991 (1.00)	0.893 (1.00)	1 (1.00)

'amp_1q22' versus 'YEARS_TO_BIRTH'

P value = 0.0122 (Wilcoxon-test), Q value = 0.046

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

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 1(1Q22) MUTATED	37	63.5 (4.5)
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 = 0.00016

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

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 1(1Q22) MUTATED	4	30	5
AMP PEAK 1(1Q22) WILD-TYPE	184	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 = 0.000557 (Fisher's exact test), Q value = 0.0042

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

nPatients	0	1
ALL	342	77
AMP PEAK 1(1Q22) MUTATED	21	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 = 0.033 (Fisher's exact test), Q value = 0.095

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

nPatients	NO	YES
ALL	378	57
AMP PEAK 1(1Q22) MUTATED	26	9
AMP PEAK 1(1Q22) WILD-TYPE	352	48

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

'amp_1q22' versus 'HISTOLOGICAL_TYPE'

P value = 0.0191 (Fisher's exact test), Q value = 0.065

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

nPatients	PROSTATE ADENOCARCINOMA OTHER SUBTYPE	PROSTATE ADENOCARCINOMA ACINAR TYPE
ALL	14	477
AMP PEAK 1(1Q22) MUTATED	4	35
AMP PEAK 1(1Q22) WILD-TYPE	10	442

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

'amp_1q22' versus 'RESIDUAL_TUMOR'

P value = 0.0534 (Fisher's exact test), Q value = 0.14

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

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 1(1Q22) MUTATED	19	19	0	0
AMP PEAK 1(1Q22) WILD-TYPE	293	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 = 0.000171 (Wilcoxon-test), Q value = 0.0018

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

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 1(1Q22) MUTATED	36	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 = 3.24e-07 (Wilcoxon-test), Q value = 1.2e-05

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

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 1(1Q22) MUTATED	39	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 = 0.00282 (Wilcoxon-test), Q value = 0.015

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

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 2(3Q21.3) MUTATED	71	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 = 0.00016

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

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 2(3Q21.3) MUTATED	12	56	5
AMP PEAK 2(3Q21.3) WILD-TYPE	176	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 = 0.0012 (Fisher's exact test), Q value = 0.0075

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

nPatients	0	1
ALL	342	77
AMP PEAK 2(3Q21.3) MUTATED	47	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 = 0.0265 (Fisher's exact test), Q value = 0.082

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

nPatients	NO	YES
ALL	378	57
AMP PEAK 2(3Q21.3) MUTATED	49	14
AMP PEAK 2(3Q21.3) WILD-TYPE	329	43

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 = 0.00044 (Fisher's exact test), Q value = 0.0037

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

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 2(3Q21.3) MUTATED	32	31	2	5
AMP PEAK 2(3Q21.3) WILD-TYPE	280	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 = 0.000105 (Wilcoxon-test), Q value = 0.0012

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

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 2(3Q21.3) MUTATED	65	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 = 7.01e-11 (Wilcoxon-test), Q value = 1.3e-08

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

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 2(3Q21.3) MUTATED	74	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 = 0.0247 (Wilcoxon-test), Q value = 0.078

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

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 3(3Q26.2) MUTATED	82	62.5 (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 = 0.00016

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

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 3(3Q26.2) MUTATED	16	62	6
AMP PEAK 3(3Q26.2) WILD-TYPE	172	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 = 0.000636 (Fisher's exact test), Q value = 0.0046

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

nPatients	0	1
ALL	342	77
AMP PEAK 3(3Q26.2) MUTATED	54	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 'RADIATION_THERAPY'

P value = 0.0871 (Fisher's exact test), Q value = 0.19

Table S19. Gene #3: 'amp_3q26.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
AMP PEAK 3(3Q26.2) MUTATED	58	14
AMP PEAK 3(3Q26.2) WILD-TYPE	320	43

Figure S19. Get High-res Image Gene #3: 'amp_3q26.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_3q26.2' versus 'RESIDUAL_TUMOR'

P value = 3e-04 (Fisher's exact test), Q value = 0.0027

Table S20. Gene #3: 'amp_3q26.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 3(3Q26.2) MUTATED	37	38	2	4
AMP PEAK 3(3Q26.2) WILD-TYPE	275	105	3	11

Figure S20. 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 = 5.74e-05 (Wilcoxon-test), Q value = 0.00075

Table S21. Gene #3: 'amp_3q26.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 3(3Q26.2) MUTATED	76	1.0 (1.9)
AMP PEAK 3(3Q26.2) WILD-TYPE	325	0.3 (1.2)

Figure S21. 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 = 2.17e-09 (Wilcoxon-test), Q value = 1.7e-07

Table S22. Gene #3: 'amp_3q26.2' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 3(3Q26.2) MUTATED	85	8.2 (1.0)
AMP PEAK 3(3Q26.2) WILD-TYPE	406	7.5 (1.0)

Figure S22. Get High-res Image Gene #3: 'amp_3q26.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_3q26.2' versus 'PSA_VALUE'

P value = 0.0511 (Wilcoxon-test), Q value = 0.13

Table S23. Gene #3: 'amp_3q26.2' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
AMP PEAK 3(3Q26.2) MUTATED	74	2.7 (8.0)
AMP PEAK 3(3Q26.2) WILD-TYPE	360	1.6 (17.2)

Figure S23. Get High-res Image Gene #3: 'amp_3q26.2' versus Clinical Feature #10: 'PSA_VALUE'

'amp_4p16.3' versus 'YEARS_TO_BIRTH'

P value = 0.0452 (Wilcoxon-test), Q value = 0.12

Table S24. Gene #4: 'amp_4p16.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 4(4P16.3) MUTATED	18	63.7 (6.6)
AMP PEAK 4(4P16.3) WILD-TYPE	462	60.9 (6.8)

Figure S24. 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 = 0.00076 (Fisher's exact test), Q value = 0.0052

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

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 4(4P16.3) MUTATED	1	16	2
AMP PEAK 4(4P16.3) WILD-TYPE	187	271	8

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

'amp_4p16.3' versus 'GLEASON_SCORE'

P value = 0.00843 (Wilcoxon-test), Q value = 0.035

Table S26. Gene #4: 'amp_4p16.3' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 4(4P16.3) MUTATED	19	8.2 (1.0)
AMP PEAK 4(4P16.3) WILD-TYPE	472	7.6 (1.0)

Figure S26. Get High-res Image Gene #4: 'amp_4p16.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_4q13.3' versus 'YEARS_TO_BIRTH'

P value = 0.019 (Wilcoxon-test), Q value = 0.065

Table S27. Gene #5: 'amp_4q13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 5(4Q13.3) MUTATED	20	64.6 (5.5)
AMP PEAK 5(4Q13.3) WILD-TYPE	460	60.8 (6.8)

Figure S27. 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 = 0.00184 (Fisher's exact test), Q value = 0.011

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

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 5(4Q13.3) MUTATED	2	18	2
AMP PEAK 5(4Q13.3) WILD-TYPE	186	269	8

Figure S28. 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 = 0.000521 (Fisher's exact test), Q value = 0.004

Table S29. Gene #5: 'amp_4q13.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 5(4Q13.3) MUTATED	11	11
AMP PEAK 5(4Q13.3) WILD-TYPE	331	66

Figure S29. Get High-res Image Gene #5: 'amp_4q13.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_4q13.3' versus 'RESIDUAL_TUMOR'

P value = 0.00507 (Fisher's exact test), Q value = 0.023

Table S30. Gene #5: 'amp_4q13.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 5(4Q13.3) MUTATED	7	14	0	1
AMP PEAK 5(4Q13.3) WILD-TYPE	305	129	5	14

Figure S30. 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 = 5.14e-05 (Wilcoxon-test), Q value = 0.00068

Table S31. Gene #5: 'amp_4q13.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 5(4Q13.3) MUTATED	21	1.2 (1.7)
AMP PEAK 5(4Q13.3) WILD-TYPE	380	0.4 (1.3)

Figure S31. 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 = 0.000256 (Wilcoxon-test), Q value = 0.0024

Table S32. Gene #5: 'amp_4q13.3' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 5(4Q13.3) MUTATED	22	8.4 (1.0)
AMP PEAK 5(4Q13.3) WILD-TYPE	469	7.6 (1.0)

Figure S32. Get High-res Image Gene #5: 'amp_4q13.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_5q35.3' versus 'YEARS_TO_BIRTH'

P value = 2.6e-07 (Wilcoxon-test), Q value = 1e-05

Table S33. Gene #6: 'amp_5q35.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 6(5Q35.3) MUTATED	28	67.1 (4.0)
AMP PEAK 6(5Q35.3) WILD-TYPE	452	60.6 (6.8)

Figure S33. 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 = 0.00019 (Fisher's exact test), Q value = 0.002

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

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 6(5Q35.3) MUTATED	2	24	2
AMP PEAK 6(5Q35.3) WILD-TYPE	186	263	8

Figure S34. 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 = 0.000717 (Fisher's exact test), Q value = 0.0051

Table S35. Gene #6: 'amp_5q35.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 6(5Q35.3) MUTATED	14	12
AMP PEAK 6(5Q35.3) WILD-TYPE	328	65

Figure S35. Get High-res Image Gene #6: 'amp_5q35.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_5q35.3' versus 'RESIDUAL_TUMOR'

P value = 0.0621 (Fisher's exact test), Q value = 0.15

Table S36. Gene #6: 'amp_5q35.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 6(5Q35.3) MUTATED	13	13	1	1
AMP PEAK 6(5Q35.3) WILD-TYPE	299	130	4	14

Figure S36. 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 = 6.35e-05 (Wilcoxon-test), Q value = 0.00081

Table S37. Gene #6: 'amp_5q35.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 6(5Q35.3) MUTATED	25	1.8 (3.5)
AMP PEAK 6(5Q35.3) WILD-TYPE	376	0.3 (1.0)

Figure S37. 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 = 3.64e-05 (Wilcoxon-test), Q value = 5e-04

Table S38. Gene #6: 'amp_5q35.3' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 6(5Q35.3) MUTATED	28	8.4 (0.8)
AMP PEAK 6(5Q35.3) WILD-TYPE	463	7.6 (1.0)

Figure S38. Get High-res Image Gene #6: 'amp_5q35.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_7p14.3' versus 'YEARS_TO_BIRTH'

P value = 0.0107 (Wilcoxon-test), Q value = 0.042

Table S39. Gene #7: 'amp_7p14.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 7(7P14.3) MUTATED	100	62.4 (6.7)
AMP PEAK 7(7P14.3) WILD-TYPE	380	60.6 (6.8)

Figure S39. 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 = 0.0183 (Fisher's exact test), Q value = 0.064

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

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 7(7P14.3) MUTATED	28	73	2
AMP PEAK 7(7P14.3) WILD-TYPE	160	214	8

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

'amp_7p14.3' versus 'RESIDUAL_TUMOR'

P value = 0.00172 (Fisher's exact test), Q value = 0.01

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

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 7(7P14.3) MUTATED	50	45	1	4
AMP PEAK 7(7P14.3) WILD-TYPE	262	98	4	11

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

'amp_7p14.3' versus 'GLEASON_SCORE'

P value = 0.000205 (Wilcoxon-test), Q value = 0.002

Table S42. Gene #7: 'amp_7p14.3' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 7(7P14.3) MUTATED	103	8.0 (1.1)
AMP PEAK 7(7P14.3) WILD-TYPE	388	7.5 (1.0)

Figure S42. Get High-res Image Gene #7: 'amp_7p14.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_7q22.1' versus 'YEARS_TO_BIRTH'

P value = 0.00818 (Wilcoxon-test), Q value = 0.034

Table S43. Gene #8: 'amp_7q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 8(7Q22.1) MUTATED	98	62.4 (6.8)
AMP PEAK 8(7Q22.1) WILD-TYPE	382	60.6 (6.8)

Figure S43. 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 = 0.0632 (Fisher's exact test), Q value = 0.15

Table S44. Gene #8: 'amp_7q22.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 8(7Q22.1) MUTATED	29	69	2
AMP PEAK 8(7Q22.1) WILD-TYPE	159	218	8

Figure S44. Get High-res Image Gene #8: 'amp_7q22.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_7q22.1' versus 'RESIDUAL_TUMOR'

P value = 0.00326 (Fisher's exact test), Q value = 0.016

Table S45. Gene #8: 'amp_7q22.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 8(7Q22.1) MUTATED	50	44	1	3
AMP PEAK 8(7Q22.1) WILD-TYPE	262	99	4	12

Figure S45. Get High-res Image Gene #8: 'amp_7q22.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_7q22.1' versus 'GLEASON_SCORE'

P value = 0.000185 (Wilcoxon-test), Q value = 0.002

Table S46. Gene #8: 'amp_7q22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 8(7Q22.1) MUTATED	100	8.0 (1.1)
AMP PEAK 8(7Q22.1) WILD-TYPE	391	7.5 (1.0)

Figure S46. Get High-res Image Gene #8: 'amp_7q22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_8p11.23' versus 'YEARS_TO_BIRTH'

P value = 0.000488 (Wilcoxon-test), Q value = 0.0038

Table S47. Gene #9: 'amp_8p11.23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 9(8P11.23) MUTATED	64	63.7 (6.5)
AMP PEAK 9(8P11.23) WILD-TYPE	416	60.6 (6.8)

Figure S47. 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 = 0.00364 (Fisher's exact test), Q value = 0.018

Table S48. Gene #9: 'amp_8p11.23' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 9(8P11.23) MUTATED	15	49	3
AMP PEAK 9(8P11.23) WILD-TYPE	173	238	7

Figure S48. Get High-res Image Gene #9: 'amp_8p11.23' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_8p11.23' versus 'RESIDUAL_TUMOR'

P value = 0.0119 (Fisher's exact test), Q value = 0.046

Table S49. Gene #9: 'amp_8p11.23' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 9(8P11.23) MUTATED	31	29	1	3
AMP PEAK 9(8P11.23) WILD-TYPE	281	114	4	12

Figure S49. Get High-res Image Gene #9: 'amp_8p11.23' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_8p11.23' versus 'GLEASON_SCORE'

P value = 1.67e-06 (Wilcoxon-test), Q value = 5e-05

Table S50. Gene #9: 'amp_8p11.23' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 9(8P11.23) MUTATED	67	8.2 (1.0)
AMP PEAK 9(8P11.23) WILD-TYPE	424	7.5 (1.0)

Figure S50. Get High-res Image Gene #9: 'amp_8p11.23' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_8q22.1' versus 'YEARS_TO_BIRTH'

P value = 0.0909 (Wilcoxon-test), Q value = 0.2

Table S51. Gene #10: 'amp_8q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 10(8Q22.1) MUTATED	153	61.7 (6.3)
AMP PEAK 10(8Q22.1) WILD-TYPE	327	60.6 (7.0)

Figure S51. 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 = 0.00016

Table S52. Gene #10: 'amp_8q22.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 10(8Q22.1) MUTATED	33	116	6
AMP PEAK 10(8Q22.1) WILD-TYPE	155	171	4

Figure S52. 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 = 0.00142 (Fisher's exact test), Q value = 0.0087

Table S53. Gene #10: 'amp_8q22.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 10(8Q22.1) MUTATED	106	39
AMP PEAK 10(8Q22.1) WILD-TYPE	236	38

Figure S53. Get High-res Image Gene #10: 'amp_8q22.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_8q22.1' versus 'RADIATION_THERAPY'

P value = 0.00877 (Fisher's exact test), Q value = 0.036

Table S54. Gene #10: 'amp_8q22.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
AMP PEAK 10(8Q22.1) MUTATED	110	27
AMP PEAK 10(8Q22.1) WILD-TYPE	268	30

Figure S54. Get High-res Image Gene #10: 'amp_8q22.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_8q22.1' versus 'RESIDUAL_TUMOR'

P value = 2e-05 (Fisher's exact test), Q value = 0.00029

Table S55. Gene #10: 'amp_8q22.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 10(8Q22.1) MUTATED	77	66	1	7
AMP PEAK 10(8Q22.1) WILD-TYPE	235	77	4	8

Figure S55. 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 = 0.000483 (Wilcoxon-test), Q value = 0.0038

Table S56. Gene #10: 'amp_8q22.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 10(8Q22.1) MUTATED	138	0.7 (1.6)
AMP PEAK 10(8Q22.1) WILD-TYPE	263	0.3 (1.2)

Figure S56. 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 = 2.43e-13 (Wilcoxon-test), Q value = 1.7e-10

Table S57. Gene #10: 'amp_8q22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 10(8Q22.1) MUTATED	156	8.1 (1.0)
AMP PEAK 10(8Q22.1) WILD-TYPE	335	7.4 (0.9)

Figure S57. Get High-res Image Gene #10: 'amp_8q22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_8q22.1' versus 'PSA_VALUE'

P value = 0.0606 (Wilcoxon-test), Q value = 0.15

Table S58. Gene #10: 'amp_8q22.1' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
AMP PEAK 10(8Q22.1) MUTATED	136	3.8 (28.0)
AMP PEAK 10(8Q22.1) WILD-TYPE	298	0.9 (3.8)

Figure S58. Get High-res Image Gene #10: 'amp_8q22.1' versus Clinical Feature #10: 'PSA_VALUE'

'amp_8q24.21' versus 'YEARS_TO_BIRTH'

P value = 0.057 (Wilcoxon-test), Q value = 0.14

Table S59. Gene #11: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 11(8Q24.21) MUTATED	147	61.9 (6.3)
AMP PEAK 11(8Q24.21) WILD-TYPE	333	60.6 (7.0)

Figure S59. 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 = 0.00016

Table S60. Gene #11: 'amp_8q24.21' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 11(8Q24.21) MUTATED	33	111	6
AMP PEAK 11(8Q24.21) WILD-TYPE	155	176	4

Figure S60. 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 = 0.000738 (Fisher's exact test), Q value = 0.0052

Table S61. Gene #11: 'amp_8q24.21' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 11(8Q24.21) MUTATED	101	39
AMP PEAK 11(8Q24.21) WILD-TYPE	241	38

Figure S61. Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_8q24.21' versus 'RADIATION_THERAPY'

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

Table S62. Gene #11: 'amp_8q24.21' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
AMP PEAK 11(8Q24.21) MUTATED	105	24
AMP PEAK 11(8Q24.21) WILD-TYPE	273	33

Figure S62. Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_8q24.21' versus 'RESIDUAL_TUMOR'

P value = 0.00024 (Fisher's exact test), Q value = 0.0023

Table S63. Gene #11: 'amp_8q24.21' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 11(8Q24.21) MUTATED	76	62	1	7
AMP PEAK 11(8Q24.21) WILD-TYPE	236	81	4	8

Figure S63. 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 = 0.000147 (Wilcoxon-test), Q value = 0.0016

Table S64. Gene #11: 'amp_8q24.21' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 11(8Q24.21) MUTATED	133	0.7 (1.4)
AMP PEAK 11(8Q24.21) WILD-TYPE	268	0.3 (1.3)

Figure S64. 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 = 1.53e-12 (Wilcoxon-test), Q value = 3.6e-10

Table S65. Gene #11: 'amp_8q24.21' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 11(8Q24.21) MUTATED	151	8.1 (1.0)
AMP PEAK 11(8Q24.21) WILD-TYPE	340	7.4 (0.9)

Figure S65. Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_8q24.21' versus 'PSA_VALUE'

P value = 0.0321 (Wilcoxon-test), Q value = 0.094

Table S66. Gene #11: 'amp_8q24.21' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
AMP PEAK 11(8Q24.21) MUTATED	129	4.0 (28.7)
AMP PEAK 11(8Q24.21) WILD-TYPE	305	0.9 (3.7)

Figure S66. Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #10: 'PSA_VALUE'

'amp_9q33.3' versus 'YEARS_TO_BIRTH'

P value = 0.0274 (Wilcoxon-test), Q value = 0.084

Table S67. Gene #12: 'amp_9q33.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 12(9Q33.3) MUTATED	59	62.9 (6.4)
AMP PEAK 12(9Q33.3) WILD-TYPE	421	60.7 (6.8)

Figure S67. 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 = 0.00016

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

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 12(9Q33.3) MUTATED	5	52	3
AMP PEAK 12(9Q33.3) WILD-TYPE	183	235	7

Figure S68. 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 = 1.2e-08 (Fisher's exact test), Q value = 6.6e-07

Table S69. Gene #12: 'amp_9q33.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 12(9Q33.3) MUTATED	30	28
AMP PEAK 12(9Q33.3) WILD-TYPE	312	49

Figure S69. Get High-res Image Gene #12: 'amp_9q33.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_9q33.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0828 (Fisher's exact test), Q value = 0.19

Table S70. Gene #12: 'amp_9q33.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	PROSTATE ADENOCARCINOMA OTHER SUBTYPE	PROSTATE ADENOCARCINOMA ACINAR TYPE
ALL	14	477
AMP PEAK 12(9Q33.3) MUTATED	4	57
AMP PEAK 12(9Q33.3) WILD-TYPE	10	420

Figure S70. Get High-res Image Gene #12: 'amp_9q33.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_9q33.3' versus 'RESIDUAL_TUMOR'

P value = 0.00078 (Fisher's exact test), Q value = 0.0053

Table S71. Gene #12: 'amp_9q33.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 12(9Q33.3) MUTATED	26	31	1	1
AMP PEAK 12(9Q33.3) WILD-TYPE	286	112	4	14

Figure S71. 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 = 2.74e-10 (Wilcoxon-test), Q value = 3.3e-08

Table S72. Gene #12: 'amp_9q33.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 12(9Q33.3) MUTATED	58	1.3 (2.5)
AMP PEAK 12(9Q33.3) WILD-TYPE	343	0.3 (1.0)

Figure S72. 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 = 1.3e-12 (Wilcoxon-test), Q value = 3.6e-10

Table S73. Gene #12: 'amp_9q33.3' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 12(9Q33.3) MUTATED	61	8.5 (0.8)
AMP PEAK 12(9Q33.3) WILD-TYPE	430	7.5 (1.0)

Figure S73. Get High-res Image Gene #12: 'amp_9q33.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_11q13.2' versus 'YEARS_TO_BIRTH'

P value = 0.000569 (Wilcoxon-test), Q value = 0.0042

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

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 13(11Q13.2) MUTATED	45	64.1 (5.9)
AMP PEAK 13(11Q13.2) WILD-TYPE	435	60.7 (6.8)

Figure S74. 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 = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S75. Gene #13: 'amp_11q13.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 13(11Q13.2) MUTATED	5	39	3
AMP PEAK 13(11Q13.2) WILD-TYPE	183	248	7

Figure S75. 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 = 6.26e-06 (Fisher's exact test), Q value = 0.00016

Table S76. Gene #13: 'amp_11q13.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 13(11Q13.2) MUTATED	23	20
AMP PEAK 13(11Q13.2) WILD-TYPE	319	57

Figure S76. Get High-res Image Gene #13: 'amp_11q13.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_11q13.2' versus 'RADIATION_THERAPY'

P value = 0.0963 (Fisher's exact test), Q value = 0.21

Table S77. Gene #13: 'amp_11q13.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
AMP PEAK 13(11Q13.2) MUTATED	33	9
AMP PEAK 13(11Q13.2) WILD-TYPE	345	48

Figure S77. Get High-res Image Gene #13: 'amp_11q13.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_11q13.2' versus 'RESIDUAL_TUMOR'

P value = 0.00303 (Fisher's exact test), Q value = 0.015

Table S78. Gene #13: 'amp_11q13.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 13(11Q13.2) MUTATED	20	25	0	2
AMP PEAK 13(11Q13.2) WILD-TYPE	292	118	5	13

Figure S78. 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 = 2.87e-07 (Wilcoxon-test), Q value = 1.1e-05

Table S79. Gene #13: 'amp_11q13.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 13(11Q13.2) MUTATED	41	1.4 (2.8)
AMP PEAK 13(11Q13.2) WILD-TYPE	360	0.3 (1.0)

Figure S79. 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 = 2.28e-08 (Wilcoxon-test), Q value = 1.1e-06

Table S80. Gene #13: 'amp_11q13.2' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 13(11Q13.2) MUTATED	47	8.4 (0.9)
AMP PEAK 13(11Q13.2) WILD-TYPE	444	7.5 (1.0)

Figure S80. Get High-res Image Gene #13: 'amp_11q13.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_12q23.1' versus 'YEARS_TO_BIRTH'

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

Table S81. Gene #14: 'amp_12q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 14(12Q23.1) MUTATED	35	62.8 (6.5)
AMP PEAK 14(12Q23.1) WILD-TYPE	445	60.8 (6.8)

Figure S81. 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 = 7e-04 (Fisher's exact test), Q value = 0.005

Table S82. Gene #14: 'amp_12q23.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 14(12Q23.1) MUTATED	4	31	1
AMP PEAK 14(12Q23.1) WILD-TYPE	184	256	9

Figure S82. 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 = 0.000204 (Fisher's exact test), Q value = 0.002

Table S83. Gene #14: 'amp_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 14(12Q23.1) MUTATED	16	14
AMP PEAK 14(12Q23.1) WILD-TYPE	326	63

Figure S83. Get High-res Image Gene #14: 'amp_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_12q23.1' versus 'RADIATION_THERAPY'

P value = 0.012 (Fisher's exact test), Q value = 0.046

Table S84. Gene #14: 'amp_12q23.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
AMP PEAK 14(12Q23.1) MUTATED	22	9
AMP PEAK 14(12Q23.1) WILD-TYPE	356	48

Figure S84. Get High-res Image Gene #14: 'amp_12q23.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_12q23.1' versus 'RESIDUAL_TUMOR'

P value = 3e-04 (Fisher's exact test), Q value = 0.0027

Table S85. Gene #14: 'amp_12q23.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 14(12Q23.1) MUTATED	13	22	1	0
AMP PEAK 14(12Q23.1) WILD-TYPE	299	121	4	15

Figure S85. 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 = 2.77e-05 (Wilcoxon-test), Q value = 0.00039

Table S86. Gene #14: 'amp_12q23.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 14(12Q23.1) MUTATED	29	1.3 (2.4)
AMP PEAK 14(12Q23.1) WILD-TYPE	372	0.4 (1.2)

Figure S86. 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 = 9.96e-07 (Wilcoxon-test), Q value = 3.2e-05

Table S87. Gene #14: 'amp_12q23.1' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 14(12Q23.1) MUTATED	36	8.4 (1.0)
AMP PEAK 14(12Q23.1) WILD-TYPE	455	7.5 (1.0)

Figure S87. Get High-res Image Gene #14: 'amp_12q23.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_13q12.11' versus 'YEARS_TO_BIRTH'

P value = 0.000412 (Wilcoxon-test), Q value = 0.0036

Table S88. Gene #15: 'amp_13q12.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 15(13Q12.11) MUTATED	24	65.5 (4.2)
AMP PEAK 15(13Q12.11) WILD-TYPE	456	60.7 (6.8)

Figure S88. 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 = 0.0045 (Fisher's exact test), Q value = 0.021

Table S89. Gene #15: 'amp_13q12.11' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 15(13Q12.11) MUTATED	5	17	3
AMP PEAK 15(13Q12.11) WILD-TYPE	183	270	7

Figure S89. Get High-res Image Gene #15: 'amp_13q12.11' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_13q12.11' versus 'HISTOLOGICAL_TYPE'

P value = 0.0293 (Fisher's exact test), Q value = 0.087

Table S90. Gene #15: 'amp_13q12.11' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	PROSTATE ADENOCARCINOMA OTHER SUBTYPE	PROSTATE ADENOCARCINOMA ACINAR TYPE
ALL	14	477
AMP PEAK 15(13Q12.11) MUTATED	3	22
AMP PEAK 15(13Q12.11) WILD-TYPE	11	455

Figure S90. 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 = 0.0836 (Wilcoxon-test), Q value = 0.19

Table S91. Gene #15: 'amp_13q12.11' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 15(13Q12.11) MUTATED	21	0.7 (1.4)
AMP PEAK 15(13Q12.11) WILD-TYPE	380	0.4 (1.4)

Figure S91. 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 = 0.0107 (Wilcoxon-test), Q value = 0.042

Table S92. Gene #15: 'amp_13q12.11' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 15(13Q12.11) MUTATED	25	8.1 (1.1)
AMP PEAK 15(13Q12.11) WILD-TYPE	466	7.6 (1.0)

Figure S92. Get High-res Image Gene #15: 'amp_13q12.11' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_14q21.1' versus 'YEARS_TO_BIRTH'

P value = 0.0368 (Wilcoxon-test), Q value = 0.1

Table S93. Gene #16: 'amp_14q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 16(14Q21.1) MUTATED	28	63.4 (5.6)
AMP PEAK 16(14Q21.1) WILD-TYPE	452	60.8 (6.9)

Figure S93. 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 = 0.0691 (Fisher's exact test), Q value = 0.16

Table S94. Gene #16: 'amp_14q21.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 16(14Q21.1) MUTATED	6	24	0
AMP PEAK 16(14Q21.1) WILD-TYPE	182	263	10

Figure S94. 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 = 0.0148 (Fisher's exact test), Q value = 0.054

Table S95. Gene #16: 'amp_14q21.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 16(14Q21.1) MUTATED	16	10
AMP PEAK 16(14Q21.1) WILD-TYPE	326	67

Figure S95. Get High-res Image Gene #16: 'amp_14q21.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_14q21.1' versus 'RADIATION_THERAPY'

P value = 0.00319 (Fisher's exact test), Q value = 0.016

Table S96. Gene #16: 'amp_14q21.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
AMP PEAK 16(14Q21.1) MUTATED	17	9
AMP PEAK 16(14Q21.1) WILD-TYPE	361	48

Figure S96. 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 = 0.0055 (Wilcoxon-test), Q value = 0.024

Table S97. Gene #16: 'amp_14q21.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 16(14Q21.1) MUTATED	26	1.2 (2.0)
AMP PEAK 16(14Q21.1) WILD-TYPE	375	0.4 (1.3)

Figure S97. 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 = 7.74e-05 (Wilcoxon-test), Q value = 0.00094

Table S98. Gene #16: 'amp_14q21.1' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 16(14Q21.1) MUTATED	30	8.3 (0.9)
AMP PEAK 16(14Q21.1) WILD-TYPE	461	7.6 (1.0)

Figure S98. Get High-res Image Gene #16: 'amp_14q21.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_15q11.2' versus 'Time to Death'

P value = 0.0932 (logrank test), Q value = 0.2

Table S99. Gene #17: 'amp_15q11.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	489	9	0.7 - 165.2 (28.8)
AMP PEAK 17(15Q11.2) MUTATED	15	1	4.3 - 69.3 (32.0)
AMP PEAK 17(15Q11.2) WILD-TYPE	474	8	0.7 - 165.2 (28.8)

Figure S99. 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 = 0.085 (Wilcoxon-test), Q value = 0.19

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

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 17(15Q11.2) MUTATED	14	63.8 (7.7)
AMP PEAK 17(15Q11.2) WILD-TYPE	466	60.9 (6.8)

Figure S100. 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 = 0.118 (Fisher's exact test), Q value = 0.24

Table S101. Gene #17: 'amp_15q11.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 17(15Q11.2) MUTATED	3	11	1
AMP PEAK 17(15Q11.2) WILD-TYPE	185	276	9

Figure S101. 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 = 0.000143 (Fisher's exact test), Q value = 0.0016

Table S102. Gene #17: 'amp_15q11.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 17(15Q11.2) MUTATED	5	9
AMP PEAK 17(15Q11.2) WILD-TYPE	337	68

Figure S102. Get High-res Image Gene #17: 'amp_15q11.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_15q11.2' versus 'RADIATION_THERAPY'

P value = 0.0586 (Fisher's exact test), Q value = 0.15

Table S103. Gene #17: 'amp_15q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
AMP PEAK 17(15Q11.2) MUTATED	8	4
AMP PEAK 17(15Q11.2) WILD-TYPE	370	53

Figure S103. Get High-res Image Gene #17: 'amp_15q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_15q11.2' versus 'RESIDUAL_TUMOR'

P value = 0.0344 (Fisher's exact test), Q value = 0.097

Table S104. Gene #17: 'amp_15q11.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 17(15Q11.2) MUTATED	5	10	0	0
AMP PEAK 17(15Q11.2) WILD-TYPE	307	133	5	15

Figure S104. 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 = 4.27e-06 (Wilcoxon-test), Q value = 0.00012

Table S105. Gene #17: 'amp_15q11.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 17(15Q11.2) MUTATED	14	1.4 (1.3)
AMP PEAK 17(15Q11.2) WILD-TYPE	387	0.4 (1.4)

Figure S105. 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 = 0.00307 (Wilcoxon-test), Q value = 0.016

Table S106. Gene #17: 'amp_15q11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 17(15Q11.2) MUTATED	15	8.4 (1.0)
AMP PEAK 17(15Q11.2) WILD-TYPE	476	7.6 (1.0)

Figure S106. Get High-res Image Gene #17: 'amp_15q11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_16q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.0262 (Wilcoxon-test), Q value = 0.082

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

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 18(16Q11.2) MUTATED	28	63.6 (6.2)
AMP PEAK 18(16Q11.2) WILD-TYPE	452	60.8 (6.8)

Figure S107. 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 = 0.00029 (Fisher's exact test), Q value = 0.0027

Table S108. Gene #18: 'amp_16q11.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 18(16Q11.2) MUTATED	2	27	1
AMP PEAK 18(16Q11.2) WILD-TYPE	186	260	9

Figure S108. 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 = 0.0728 (Fisher's exact test), Q value = 0.17

Table S109. Gene #18: 'amp_16q11.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 18(16Q11.2) MUTATED	19	9
AMP PEAK 18(16Q11.2) WILD-TYPE	323	68

Figure S109. Get High-res Image Gene #18: 'amp_16q11.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_16q11.2' versus 'RADIATION_THERAPY'

P value = 0.0539 (Fisher's exact test), Q value = 0.14

Table S110. Gene #18: 'amp_16q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
AMP PEAK 18(16Q11.2) MUTATED	16	6
AMP PEAK 18(16Q11.2) WILD-TYPE	362	51

Figure S110. Get High-res Image Gene #18: 'amp_16q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_16q11.2' versus 'RESIDUAL_TUMOR'

P value = 0.038 (Fisher's exact test), Q value = 0.11

Table S111. Gene #18: 'amp_16q11.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 18(16Q11.2) MUTATED	13	16	0	1
AMP PEAK 18(16Q11.2) WILD-TYPE	299	127	5	14

Figure S111. 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 = 0.0589 (Wilcoxon-test), Q value = 0.15

Table S112. Gene #18: 'amp_16q11.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 18(16Q11.2) MUTATED	27	0.7 (1.6)
AMP PEAK 18(16Q11.2) WILD-TYPE	374	0.4 (1.3)

Figure S112. 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 = 1.57e-06 (Wilcoxon-test), Q value = 4.9e-05

Table S113. Gene #18: 'amp_16q11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 18(16Q11.2) MUTATED	30	8.5 (0.9)
AMP PEAK 18(16Q11.2) WILD-TYPE	461	7.5 (1.0)

Figure S113. Get High-res Image Gene #18: 'amp_16q11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_16q11.2' versus 'PSA_VALUE'

P value = 0.0205 (Wilcoxon-test), Q value = 0.069

Table S114. Gene #18: 'amp_16q11.2' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
AMP PEAK 18(16Q11.2) MUTATED	24	1.3 (2.6)
AMP PEAK 18(16Q11.2) WILD-TYPE	410	1.8 (16.4)

Figure S114. Get High-res Image Gene #18: 'amp_16q11.2' versus Clinical Feature #10: 'PSA_VALUE'

'amp_17q23.2' versus 'Time to Death'

P value = 0.12 (logrank test), Q value = 0.24

Table S115. Gene #19: 'amp_17q23.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	489	9	0.7 - 165.2 (28.8)
AMP PEAK 19(17Q23.2) MUTATED	25	1	4.3 - 109.2 (22.0)
AMP PEAK 19(17Q23.2) WILD-TYPE	464	8	0.7 - 165.2 (29.9)

Figure S115. Get High-res Image Gene #19: 'amp_17q23.2' versus Clinical Feature #1: 'Time to Death'

'amp_17q23.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00084 (Fisher's exact test), Q value = 0.0057

Table S116. Gene #19: 'amp_17q23.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 19(17Q23.2) MUTATED	2	20	2
AMP PEAK 19(17Q23.2) WILD-TYPE	186	267	8

Figure S116. Get High-res Image Gene #19: 'amp_17q23.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_17q23.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0217 (Fisher's exact test), Q value = 0.071

Table S117. Gene #19: 'amp_17q23.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 19(17Q23.2) MUTATED	14	9
AMP PEAK 19(17Q23.2) WILD-TYPE	328	68

Figure S117. Get High-res Image Gene #19: 'amp_17q23.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_17q23.2' versus 'RADIATION_THERAPY'

P value = 0.0539 (Fisher's exact test), Q value = 0.14

Table S118. Gene #19: 'amp_17q23.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
AMP PEAK 19(17Q23.2) MUTATED	16	6
AMP PEAK 19(17Q23.2) WILD-TYPE	362	51

Figure S118. Get High-res Image Gene #19: 'amp_17q23.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_17q23.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0293 (Fisher's exact test), Q value = 0.087

Table S119. Gene #19: 'amp_17q23.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	PROSTATE ADENOCARCINOMA OTHER SUBTYPE	PROSTATE ADENOCARCINOMA ACINAR TYPE
ALL	14	477
AMP PEAK 19(17Q23.2) MUTATED	3	22
AMP PEAK 19(17Q23.2) WILD-TYPE	11	455

Figure S119. Get High-res Image Gene #19: 'amp_17q23.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_17q23.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0111 (Wilcoxon-test), Q value = 0.043

Table S120. Gene #19: 'amp_17q23.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 19(17Q23.2) MUTATED	23	0.7 (0.9)
AMP PEAK 19(17Q23.2) WILD-TYPE	378	0.4 (1.4)

Figure S120. Get High-res Image Gene #19: 'amp_17q23.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_17q23.2' versus 'GLEASON_SCORE'

P value = 7.09e-05 (Wilcoxon-test), Q value = 0.00087

Table S121. Gene #19: 'amp_17q23.2' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 19(17Q23.2) MUTATED	25	8.4 (1.0)
AMP PEAK 19(17Q23.2) WILD-TYPE	466	7.6 (1.0)

Figure S121. Get High-res Image Gene #19: 'amp_17q23.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_17q23.2' versus 'PSA_VALUE'

P value = 0.0497 (Wilcoxon-test), Q value = 0.13

Table S122. Gene #19: 'amp_17q23.2' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
AMP PEAK 19(17Q23.2) MUTATED	22	15.6 (68.7)
AMP PEAK 19(17Q23.2) WILD-TYPE	412	1.1 (4.2)

Figure S122. Get High-res Image Gene #19: 'amp_17q23.2' versus Clinical Feature #10: 'PSA_VALUE'

'amp_19q13.43' versus 'YEARS_TO_BIRTH'

P value = 0.0301 (Wilcoxon-test), Q value = 0.089

Table S123. Gene #20: 'amp_19q13.43' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 20(19Q13.43) MUTATED	17	64.5 (6.8)
AMP PEAK 20(19Q13.43) WILD-TYPE	463	60.8 (6.8)

Figure S123. Get High-res Image Gene #20: 'amp_19q13.43' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19q13.43' versus 'PATHOLOGY_T_STAGE'

P value = 5e-04 (Fisher's exact test), Q value = 0.0038

Table S124. Gene #20: 'amp_19q13.43' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 20(19Q13.43) MUTATED	0	16	1
AMP PEAK 20(19Q13.43) WILD-TYPE	188	271	9

Figure S124. Get High-res Image Gene #20: 'amp_19q13.43' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_19q13.43' versus 'PATHOLOGY_N_STAGE'

P value = 0.022 (Fisher's exact test), Q value = 0.072

Table S125. Gene #20: 'amp_19q13.43' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 20(19Q13.43) MUTATED	10	7
AMP PEAK 20(19Q13.43) WILD-TYPE	332	70

Figure S125. Get High-res Image Gene #20: 'amp_19q13.43' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_19q13.43' versus 'HISTOLOGICAL_TYPE'

P value = 0.089 (Fisher's exact test), Q value = 0.2

Table S126. Gene #20: 'amp_19q13.43' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	PROSTATE ADENOCARCINOMA OTHER SUBTYPE	PROSTATE ADENOCARCINOMA ACINAR TYPE
ALL	14	477
AMP PEAK 20(19Q13.43) MUTATED	2	16
AMP PEAK 20(19Q13.43) WILD-TYPE	12	461

Figure S126. Get High-res Image Gene #20: 'amp_19q13.43' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_19q13.43' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0115 (Wilcoxon-test), Q value = 0.045

Table S127. Gene #20: 'amp_19q13.43' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 20(19Q13.43) MUTATED	17	1.1 (2.0)
AMP PEAK 20(19Q13.43) WILD-TYPE	384	0.4 (1.3)

Figure S127. Get High-res Image Gene #20: 'amp_19q13.43' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_19q13.43' versus 'GLEASON_SCORE'

P value = 8.97e-06 (Wilcoxon-test), Q value = 0.00016

Table S128. Gene #20: 'amp_19q13.43' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 20(19Q13.43) MUTATED	18	8.7 (0.9)
AMP PEAK 20(19Q13.43) WILD-TYPE	473	7.6 (1.0)

Figure S128. Get High-res Image Gene #20: 'amp_19q13.43' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_20q13.2' versus 'YEARS_TO_BIRTH'

P value = 0.00493 (Wilcoxon-test), Q value = 0.022

Table S129. Gene #21: 'amp_20q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 21(20Q13.2) MUTATED	41	63.7 (4.5)
AMP PEAK 21(20Q13.2) WILD-TYPE	439	60.7 (6.9)

Figure S129. Get High-res Image Gene #21: 'amp_20q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_20q13.2' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00029

Table S130. Gene #21: 'amp_20q13.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 21(20Q13.2) MUTATED	4	36	3
AMP PEAK 21(20Q13.2) WILD-TYPE	184	251	7

Figure S130. Get High-res Image Gene #21: 'amp_20q13.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_20q13.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00857 (Fisher's exact test), Q value = 0.035

Table S131. Gene #21: 'amp_20q13.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 21(20Q13.2) MUTATED	26	14
AMP PEAK 21(20Q13.2) WILD-TYPE	316	63

Figure S131. Get High-res Image Gene #21: 'amp_20q13.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_20q13.2' versus 'RADIATION_THERAPY'

P value = 0.0767 (Fisher's exact test), Q value = 0.18

Table S132. Gene #21: 'amp_20q13.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
AMP PEAK 21(20Q13.2) MUTATED	30	9
AMP PEAK 21(20Q13.2) WILD-TYPE	348	48

Figure S132. Get High-res Image Gene #21: 'amp_20q13.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_20q13.2' versus 'RESIDUAL_TUMOR'

P value = 0.0206 (Fisher's exact test), Q value = 0.069

Table S133. Gene #21: 'amp_20q13.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 21(20Q13.2) MUTATED	19	21	0	2
AMP PEAK 21(20Q13.2) WILD-TYPE	293	122	5	13

Figure S133. Get High-res Image Gene #21: 'amp_20q13.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_20q13.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00343 (Wilcoxon-test), Q value = 0.017

Table S134. Gene #21: 'amp_20q13.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 21(20Q13.2) MUTATED	38	0.8 (1.5)
AMP PEAK 21(20Q13.2) WILD-TYPE	363	0.4 (1.3)

Figure S134. Get High-res Image Gene #21: 'amp_20q13.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_20q13.2' versus 'GLEASON_SCORE'

P value = 1.51e-07 (Wilcoxon-test), Q value = 6.4e-06

Table S135. Gene #21: 'amp_20q13.2' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 21(20Q13.2) MUTATED	44	8.4 (1.0)
AMP PEAK 21(20Q13.2) WILD-TYPE	447	7.5 (1.0)

Figure S135. Get High-res Image Gene #21: 'amp_20q13.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_20q13.2' versus 'PSA_VALUE'

P value = 0.0647 (Wilcoxon-test), Q value = 0.16

Table S136. Gene #21: 'amp_20q13.2' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
AMP PEAK 21(20Q13.2) MUTATED	43	8.6 (49.2)
AMP PEAK 21(20Q13.2) WILD-TYPE	391	1.1 (4.2)

Figure S136. Get High-res Image Gene #21: 'amp_20q13.2' versus Clinical Feature #10: 'PSA_VALUE'

'amp_xp22.11' versus 'YEARS_TO_BIRTH'

P value = 0.0135 (Wilcoxon-test), Q value = 0.05

Table S137. Gene #22: 'amp_xp22.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 22(XP22.11) MUTATED	24	64.3 (5.9)
AMP PEAK 22(XP22.11) WILD-TYPE	456	60.8 (6.8)

Figure S137. Get High-res Image Gene #22: 'amp_xp22.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xp22.11' versus 'PATHOLOGY_T_STAGE'

P value = 0.00236 (Fisher's exact test), Q value = 0.013

Table S138. Gene #22: 'amp_xp22.11' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 22(XP22.11) MUTATED	4	18	3
AMP PEAK 22(XP22.11) WILD-TYPE	184	269	7

Figure S138. Get High-res Image Gene #22: 'amp_xp22.11' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_xp22.11' versus 'PATHOLOGY_N_STAGE'

P value = 0.104 (Fisher's exact test), Q value = 0.22

Table S139. Gene #22: 'amp_xp22.11' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 22(XP22.11) MUTATED	17	8
AMP PEAK 22(XP22.11) WILD-TYPE	325	69

Figure S139. Get High-res Image Gene #22: 'amp_xp22.11' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_xp22.11' versus 'RADIATION_THERAPY'

P value = 0.0436 (Fisher's exact test), Q value = 0.12

Table S140. Gene #22: 'amp_xp22.11' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
AMP PEAK 22(XP22.11) MUTATED	15	6
AMP PEAK 22(XP22.11) WILD-TYPE	363	51

Figure S140. Get High-res Image Gene #22: 'amp_xp22.11' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_xp22.11' versus 'HISTOLOGICAL_TYPE'

P value = 0.0293 (Fisher's exact test), Q value = 0.087

Table S141. Gene #22: 'amp_xp22.11' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	PROSTATE ADENOCARCINOMA OTHER SUBTYPE	PROSTATE ADENOCARCINOMA ACINAR TYPE
ALL	14	477
AMP PEAK 22(XP22.11) MUTATED	3	22
AMP PEAK 22(XP22.11) WILD-TYPE	11	455

Figure S141. Get High-res Image Gene #22: 'amp_xp22.11' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_xp22.11' versus 'RESIDUAL_TUMOR'

P value = 0.0179 (Fisher's exact test), Q value = 0.063

Table S142. Gene #22: 'amp_xp22.11' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 22(XP22.11) MUTATED	9	12	1	1
AMP PEAK 22(XP22.11) WILD-TYPE	303	131	4	14

Figure S142. Get High-res Image Gene #22: 'amp_xp22.11' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_xp22.11' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0862 (Wilcoxon-test), Q value = 0.19

Table S143. Gene #22: 'amp_xp22.11' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 22(XP22.11) MUTATED	25	0.7 (1.5)
AMP PEAK 22(XP22.11) WILD-TYPE	376	0.4 (1.4)

Figure S143. Get High-res Image Gene #22: 'amp_xp22.11' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_xp22.11' versus 'GLEASON_SCORE'

P value = 0.000988 (Wilcoxon-test), Q value = 0.0065

Table S144. Gene #22: 'amp_xp22.11' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 22(XP22.11) MUTATED	25	8.2 (0.9)
AMP PEAK 22(XP22.11) WILD-TYPE	466	7.6 (1.0)

Figure S144. Get High-res Image Gene #22: 'amp_xp22.11' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_xp22.11' versus 'YEARS_TO_BIRTH'

P value = 0.0782 (Wilcoxon-test), Q value = 0.18

Table S145. Gene #23: 'amp_xp22.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 23(XP22.11) MUTATED	23	63.3 (7.1)
AMP PEAK 23(XP22.11) WILD-TYPE	457	60.9 (6.8)

Figure S145. Get High-res Image Gene #23: 'amp_xp22.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xp22.11' versus 'PATHOLOGY_T_STAGE'

P value = 0.00217 (Fisher's exact test), Q value = 0.012

Table S146. Gene #23: 'amp_xp22.11' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 23(XP22.11) MUTATED	4	17	3
AMP PEAK 23(XP22.11) WILD-TYPE	184	270	7

Figure S146. Get High-res Image Gene #23: 'amp_xp22.11' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_xp22.11' versus 'PATHOLOGY_N_STAGE'

P value = 0.06 (Fisher's exact test), Q value = 0.15

Table S147. Gene #23: 'amp_xp22.11' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 23(XP22.11) MUTATED	16	8
AMP PEAK 23(XP22.11) WILD-TYPE	326	69

Figure S147. Get High-res Image Gene #23: 'amp_xp22.11' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_xp22.11' versus 'HISTOLOGICAL_TYPE'

P value = 0.0262 (Fisher's exact test), Q value = 0.082

Table S148. Gene #23: 'amp_xp22.11' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	PROSTATE ADENOCARCINOMA OTHER SUBTYPE	PROSTATE ADENOCARCINOMA ACINAR TYPE
ALL	14	477
AMP PEAK 23(XP22.11) MUTATED	3	21
AMP PEAK 23(XP22.11) WILD-TYPE	11	456

Figure S148. Get High-res Image Gene #23: 'amp_xp22.11' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_xp22.11' versus 'RESIDUAL_TUMOR'

P value = 0.0177 (Fisher's exact test), Q value = 0.062

Table S149. Gene #23: 'amp_xp22.11' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 23(XP22.11) MUTATED	9	12	1	1
AMP PEAK 23(XP22.11) WILD-TYPE	303	131	4	14

Figure S149. Get High-res Image Gene #23: 'amp_xp22.11' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_xp22.11' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0642 (Wilcoxon-test), Q value = 0.15

Table S150. Gene #23: 'amp_xp22.11' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 23(XP22.11) MUTATED	24	0.8 (1.5)
AMP PEAK 23(XP22.11) WILD-TYPE	377	0.4 (1.4)

Figure S150. Get High-res Image Gene #23: 'amp_xp22.11' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_xp22.11' versus 'GLEASON_SCORE'

P value = 0.00115 (Wilcoxon-test), Q value = 0.0074

Table S151. Gene #23: 'amp_xp22.11' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 23(XP22.11) MUTATED	24	8.2 (0.9)
AMP PEAK 23(XP22.11) WILD-TYPE	467	7.6 (1.0)

Figure S151. Get High-res Image Gene #23: 'amp_xp22.11' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_xp22.11' versus 'PSA_VALUE'

P value = 0.0996 (Wilcoxon-test), Q value = 0.21

Table S152. Gene #23: 'amp_xp22.11' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
AMP PEAK 23(XP22.11) MUTATED	20	0.6 (1.0)
AMP PEAK 23(XP22.11) WILD-TYPE	414	1.9 (16.4)

Figure S152. Get High-res Image Gene #23: 'amp_xp22.11' versus Clinical Feature #10: 'PSA_VALUE'

'amp_xp21.1' versus 'YEARS_TO_BIRTH'

P value = 0.00157 (Wilcoxon-test), Q value = 0.0094

Table S153. Gene #24: 'amp_xp21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 24(XP21.1) MUTATED	21	65.4 (4.9)
AMP PEAK 24(XP21.1) WILD-TYPE	459	60.8 (6.8)

Figure S153. Get High-res Image Gene #24: 'amp_xp21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xp21.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00542 (Fisher's exact test), Q value = 0.024

Table S154. Gene #24: 'amp_xp21.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 24(XP21.1) MUTATED	3	18	2
AMP PEAK 24(XP21.1) WILD-TYPE	185	269	8

Figure S154. Get High-res Image Gene #24: 'amp_xp21.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_xp21.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0499 (Fisher's exact test), Q value = 0.13

Table S155. Gene #24: 'amp_xp21.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 24(XP21.1) MUTATED	15	8
AMP PEAK 24(XP21.1) WILD-TYPE	327	69

Figure S155. Get High-res Image Gene #24: 'amp_xp21.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_xp21.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0233 (Fisher's exact test), Q value = 0.075

Table S156. Gene #24: 'amp_xp21.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	PROSTATE ADENOCARCINOMA OTHER SUBTYPE	PROSTATE ADENOCARCINOMA ACINAR TYPE
ALL	14	477
AMP PEAK 24(XP21.1) MUTATED	3	20
AMP PEAK 24(XP21.1) WILD-TYPE	11	457

Figure S156. Get High-res Image Gene #24: 'amp_xp21.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_xp21.1' versus 'RESIDUAL_TUMOR'

P value = 0.0175 (Fisher's exact test), Q value = 0.062

Table S157. Gene #24: 'amp_xp21.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 24(XP21.1) MUTATED	9	12	1	1
AMP PEAK 24(XP21.1) WILD-TYPE	303	131	4	14

Figure S157. Get High-res Image Gene #24: 'amp_xp21.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_xp21.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0463 (Wilcoxon-test), Q value = 0.12

Table S158. Gene #24: 'amp_xp21.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 24(XP21.1) MUTATED	23	0.8 (1.5)
AMP PEAK 24(XP21.1) WILD-TYPE	378	0.4 (1.4)

Figure S158. Get High-res Image Gene #24: 'amp_xp21.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'amp_xp21.1' versus 'GLEASON_SCORE'

P value = 0.000232 (Wilcoxon-test), Q value = 0.0022

Table S159. Gene #24: 'amp_xp21.1' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 24(XP21.1) MUTATED	23	8.3 (0.8)
AMP PEAK 24(XP21.1) WILD-TYPE	468	7.6 (1.0)

Figure S159. Get High-res Image Gene #24: 'amp_xp21.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_xp21.1' versus 'PSA_VALUE'

P value = 0.113 (Wilcoxon-test), Q value = 0.24

Table S160. Gene #24: 'amp_xp21.1' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
AMP PEAK 24(XP21.1) MUTATED	20	0.5 (1.0)
AMP PEAK 24(XP21.1) WILD-TYPE	414	1.9 (16.4)

Figure S160. Get High-res Image Gene #24: 'amp_xp21.1' versus Clinical Feature #10: 'PSA_VALUE'

'amp_xp21.1' versus 'RACE'

P value = 0.00745 (Fisher's exact test), Q value = 0.032

Table S161. Gene #24: 'amp_xp21.1' versus Clinical Feature #11: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	7	146
AMP PEAK 24(XP21.1) MUTATED	1	1	2
AMP PEAK 24(XP21.1) WILD-TYPE	1	6	144

Figure S161. Get High-res Image Gene #24: 'amp_xp21.1' versus Clinical Feature #11: 'RACE'

'amp_xq21.1' versus 'YEARS_TO_BIRTH'

P value = 0.0594 (Wilcoxon-test), Q value = 0.15

Table S162. Gene #25: 'amp_xq21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 25(XQ21.1) MUTATED	16	64.2 (5.5)
AMP PEAK 25(XQ21.1) WILD-TYPE	464	60.9 (6.8)

Figure S162. Get High-res Image Gene #25: 'amp_xq21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xq21.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0432 (Fisher's exact test), Q value = 0.12

Table S163. Gene #25: 'amp_xq21.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 25(XQ21.1) MUTATED	4	10	2
AMP PEAK 25(XQ21.1) WILD-TYPE	184	277	8

Figure S163. Get High-res Image Gene #25: 'amp_xq21.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_xq21.1' versus 'GLEASON_SCORE'

P value = 0.00551 (Wilcoxon-test), Q value = 0.024

Table S164. Gene #25: 'amp_xq21.1' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 25(XQ21.1) MUTATED	16	8.3 (0.9)
AMP PEAK 25(XQ21.1) WILD-TYPE	475	7.6 (1.0)

Figure S164. Get High-res Image Gene #25: 'amp_xq21.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_xq21.1' versus 'YEARS_TO_BIRTH'

P value = 0.0164 (Wilcoxon-test), Q value = 0.058

Table S165. Gene #26: 'amp_xq21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 26(XQ21.1) MUTATED	14	65.2 (5.1)
AMP PEAK 26(XQ21.1) WILD-TYPE	466	60.8 (6.8)

Figure S165. 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 = 0.0198 (Fisher's exact test), Q value = 0.068

Table S166. Gene #26: 'amp_xq21.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 26(XQ21.1) MUTATED	3	9	2
AMP PEAK 26(XQ21.1) WILD-TYPE	185	278	8

Figure S166. 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 = 0.0277 (Fisher's exact test), Q value = 0.084

Table S167. Gene #26: 'amp_xq21.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
AMP PEAK 26(XQ21.1) MUTATED	8	6
AMP PEAK 26(XQ21.1) WILD-TYPE	334	71

Figure S167. Get High-res Image Gene #26: 'amp_xq21.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'amp_xq21.1' versus 'RESIDUAL_TUMOR'

P value = 0.0798 (Fisher's exact test), Q value = 0.18

Table S168. Gene #26: 'amp_xq21.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
AMP PEAK 26(XQ21.1) MUTATED	7	5	1	1
AMP PEAK 26(XQ21.1) WILD-TYPE	305	138	4	14

Figure S168. 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 = 0.0253 (Wilcoxon-test), Q value = 0.08

Table S169. Gene #26: 'amp_xq21.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
AMP PEAK 26(XQ21.1) MUTATED	14	0.9 (1.7)
AMP PEAK 26(XQ21.1) WILD-TYPE	387	0.4 (1.4)

Figure S169. 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 = 0.00207 (Wilcoxon-test), Q value = 0.012

Table S170. Gene #26: 'amp_xq21.1' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 26(XQ21.1) MUTATED	14	8.4 (0.9)
AMP PEAK 26(XQ21.1) WILD-TYPE	477	7.6 (1.0)

Figure S170. Get High-res Image Gene #26: 'amp_xq21.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_xq21.1' versus 'RACE'

P value = 0.0273 (Fisher's exact test), Q value = 0.084

Table S171. 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 S171. Get High-res Image Gene #26: 'amp_xq21.1' versus Clinical Feature #11: 'RACE'

'amp_xq25' versus 'PATHOLOGY_T_STAGE'

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

Table S172. Gene #27: 'amp_xq25' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 27(XQ25) MUTATED	5	11	2
AMP PEAK 27(XQ25) WILD-TYPE	183	276	8

Figure S172. Get High-res Image Gene #27: 'amp_xq25' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_xq25' versus 'GLEASON_SCORE'

P value = 0.00495 (Wilcoxon-test), Q value = 0.022

Table S173. Gene #27: 'amp_xq25' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 27(XQ25) MUTATED	19	8.3 (1.0)
AMP PEAK 27(XQ25) WILD-TYPE	472	7.6 (1.0)

Figure S173. Get High-res Image Gene #27: 'amp_xq25' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_xq25' versus 'RACE'

P value = 0.0188 (Fisher's exact test), Q value = 0.065

Table S174. Gene #27: 'amp_xq25' versus Clinical Feature #11: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	7	146
AMP PEAK 27(XQ25) MUTATED	1	1	4
AMP PEAK 27(XQ25) WILD-TYPE	1	6	142

Figure S174. Get High-res Image Gene #27: 'amp_xq25' versus Clinical Feature #11: 'RACE'

'amp_xq27.1' versus 'YEARS_TO_BIRTH'

P value = 0.0216 (Wilcoxon-test), Q value = 0.071

Table S175. Gene #28: 'amp_xq27.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
AMP PEAK 28(XQ27.1) MUTATED	19	64.2 (7.1)
AMP PEAK 28(XQ27.1) WILD-TYPE	461	60.8 (6.8)

Figure S175. Get High-res Image Gene #28: 'amp_xq27.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xq27.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0774 (Fisher's exact test), Q value = 0.18

Table S176. Gene #28: 'amp_xq27.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
AMP PEAK 28(XQ27.1) MUTATED	6	10	2
AMP PEAK 28(XQ27.1) WILD-TYPE	182	277	8

Figure S176. Get High-res Image Gene #28: 'amp_xq27.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'amp_xq27.1' versus 'GLEASON_SCORE'

P value = 0.0371 (Wilcoxon-test), Q value = 0.1

Table S177. Gene #28: 'amp_xq27.1' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
AMP PEAK 28(XQ27.1) MUTATED	19	8.1 (1.0)
AMP PEAK 28(XQ27.1) WILD-TYPE	472	7.6 (1.0)

Figure S177. Get High-res Image Gene #28: 'amp_xq27.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'amp_xq27.1' versus 'PSA_VALUE'

P value = 0.114 (Wilcoxon-test), Q value = 0.24

Table S178. Gene #28: 'amp_xq27.1' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
AMP PEAK 28(XQ27.1) MUTATED	17	19.7 (78.2)
AMP PEAK 28(XQ27.1) WILD-TYPE	417	1.1 (4.2)

Figure S178. Get High-res Image Gene #28: 'amp_xq27.1' versus Clinical Feature #10: 'PSA_VALUE'

'del_1p31.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00955 (Fisher's exact test), Q value = 0.039

Table S179. Gene #29: 'del_1p31.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 1(1P31.3) MUTATED	13	44	2
DEL PEAK 1(1P31.3) WILD-TYPE	175	243	8

Figure S179. Get High-res Image Gene #29: 'del_1p31.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_1p31.3' versus 'RADIATION_THERAPY'

P value = 0.0294 (Fisher's exact test), Q value = 0.087

Table S180. Gene #29: 'del_1p31.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 1(1P31.3) MUTATED	40	12
DEL PEAK 1(1P31.3) WILD-TYPE	338	45

Figure S180. Get High-res Image Gene #29: 'del_1p31.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_1p31.3' versus 'RESIDUAL_TUMOR'

P value = 0.0701 (Fisher's exact test), Q value = 0.16

Table S181. Gene #29: 'del_1p31.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 1(1P31.3) MUTATED	30	25	1	2
DEL PEAK 1(1P31.3) WILD-TYPE	282	118	4	13

Figure S181. 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 = 0.0989 (Wilcoxon-test), Q value = 0.21

Table S182. Gene #29: 'del_1p31.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 1(1P31.3) MUTATED	51	0.5 (1.1)
DEL PEAK 1(1P31.3) WILD-TYPE	350	0.4 (1.4)

Figure S182. 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 = 0.000205 (Wilcoxon-test), Q value = 0.002

Table S183. Gene #29: 'del_1p31.3' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 1(1P31.3) MUTATED	59	8.1 (1.1)
DEL PEAK 1(1P31.3) WILD-TYPE	432	7.5 (1.0)

Figure S183. Get High-res Image Gene #29: 'del_1p31.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_1p22.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00267 (Fisher's exact test), Q value = 0.014

Table S184. Gene #30: 'del_1p22.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 2(1P22.1) MUTATED	11	44	2
DEL PEAK 2(1P22.1) WILD-TYPE	177	243	8

Figure S184. Get High-res Image Gene #30: 'del_1p22.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_1p22.1' versus 'RESIDUAL_TUMOR'

P value = 0.0911 (Fisher's exact test), Q value = 0.2

Table S185. Gene #30: 'del_1p22.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 2(1P22.1) MUTATED	29	20	0	4
DEL PEAK 2(1P22.1) WILD-TYPE	283	123	5	11

Figure S185. 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 = 0.0435 (Wilcoxon-test), Q value = 0.12

Table S186. Gene #30: 'del_1p22.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 2(1P22.1) MUTATED	47	0.6 (1.3)
DEL PEAK 2(1P22.1) WILD-TYPE	354	0.4 (1.4)

Figure S186. 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 = 0.000132 (Wilcoxon-test), Q value = 0.0015

Table S187. Gene #30: 'del_1p22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 2(1P22.1) MUTATED	58	8.1 (1.0)
DEL PEAK 2(1P22.1) WILD-TYPE	433	7.5 (1.0)

Figure S187. Get High-res Image Gene #30: 'del_1p22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_1q42.3' versus 'Time to Death'

P value = 0.000102 (logrank test), Q value = 0.0012

Table S188. Gene #32: 'del_1q42.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	489	9	0.7 - 165.2 (28.8)
DEL PEAK 4(1Q42.3) MUTATED	47	5	0.7 - 122.2 (28.5)
DEL PEAK 4(1Q42.3) WILD-TYPE	442	4	0.8 - 165.2 (29.3)

Figure S188. 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 = 0.115 (Wilcoxon-test), Q value = 0.24

Table S189. Gene #32: 'del_1q42.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
DEL PEAK 4(1Q42.3) MUTATED	47	62.4 (6.3)
DEL PEAK 4(1Q42.3) WILD-TYPE	433	60.8 (6.8)

Figure S189. Get High-res Image Gene #32: 'del_1q42.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1q42.3' versus 'RESIDUAL_TUMOR'

P value = 0.0104 (Fisher's exact test), Q value = 0.042

Table S190. Gene #32: 'del_1q42.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 4(1Q42.3) MUTATED	20	23	0	2
DEL PEAK 4(1Q42.3) WILD-TYPE	292	120	5	13

Figure S190. Get High-res Image Gene #32: 'del_1q42.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_1q42.3' versus 'GLEASON_SCORE'

P value = 0.0679 (Wilcoxon-test), Q value = 0.16

Table S191. Gene #32: 'del_1q42.3' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 4(1Q42.3) MUTATED	47	7.9 (1.0)
DEL PEAK 4(1Q42.3) WILD-TYPE	444	7.6 (1.0)

Figure S191. Get High-res Image Gene #32: 'del_1q42.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_1q42.3' versus 'PSA_VALUE'

P value = 0.0926 (Wilcoxon-test), Q value = 0.2

Table S192. Gene #32: 'del_1q42.3' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
DEL PEAK 4(1Q42.3) MUTATED	39	2.5 (7.3)
DEL PEAK 4(1Q42.3) WILD-TYPE	395	1.7 (16.6)

Figure S192. Get High-res Image Gene #32: 'del_1q42.3' versus Clinical Feature #10: 'PSA_VALUE'

'del_2p21' versus 'PATHOLOGY_T_STAGE'

P value = 0.00035 (Fisher's exact test), Q value = 0.0031

Table S193. Gene #33: 'del_2p21' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 5(2P21) MUTATED	7	35	3
DEL PEAK 5(2P21) WILD-TYPE	181	252	7

Figure S193. Get High-res Image Gene #33: 'del_2p21' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_2p21' versus 'PATHOLOGY_N_STAGE'

P value = 0.0585 (Fisher's exact test), Q value = 0.15

Table S194. Gene #33: 'del_2p21' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 5(2P21) MUTATED	30	13
DEL PEAK 5(2P21) WILD-TYPE	312	64

Figure S194. Get High-res Image Gene #33: 'del_2p21' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_2p21' versus 'RESIDUAL_TUMOR'

P value = 0.0506 (Fisher's exact test), Q value = 0.13

Table S195. Gene #33: 'del_2p21' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 5(2P21) MUTATED	21	19	1	2
DEL PEAK 5(2P21) WILD-TYPE	291	124	4	13

Figure S195. Get High-res Image Gene #33: 'del_2p21' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_2p21' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0554 (Wilcoxon-test), Q value = 0.14

Table S196. Gene #33: 'del_2p21' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 5(2P21) MUTATED	42	0.6 (1.3)
DEL PEAK 5(2P21) WILD-TYPE	359	0.4 (1.4)

Figure S196. Get High-res Image Gene #33: 'del_2p21' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_2p21' versus 'GLEASON_SCORE'

P value = 0.003 (Wilcoxon-test), Q value = 0.015

Table S197. Gene #33: 'del_2p21' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 5(2P21) MUTATED	45	8.0 (1.0)
DEL PEAK 5(2P21) WILD-TYPE	446	7.6 (1.0)

Figure S197. Get High-res Image Gene #33: 'del_2p21' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_2q22.1' versus 'YEARS_TO_BIRTH'

P value = 2.24e-05 (Wilcoxon-test), Q value = 0.00032

Table S198. Gene #34: 'del_2q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
DEL PEAK 6(2Q22.1) MUTATED	90	63.6 (5.8)
DEL PEAK 6(2Q22.1) WILD-TYPE	390	60.4 (6.9)

Figure S198. Get High-res Image Gene #34: 'del_2q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2q22.1' versus 'GLEASON_SCORE'

P value = 0.0135 (Wilcoxon-test), Q value = 0.05

Table S199. Gene #34: 'del_2q22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 6(2Q22.1) MUTATED	91	7.8 (1.0)
DEL PEAK 6(2Q22.1) WILD-TYPE	400	7.6 (1.0)

Figure S199. Get High-res Image Gene #34: 'del_2q22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_2q22.3' versus 'YEARS_TO_BIRTH'

P value = 0.00332 (Wilcoxon-test), Q value = 0.016

Table S200. Gene #35: 'del_2q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
DEL PEAK 7(2Q22.3) MUTATED	83	62.9 (6.5)
DEL PEAK 7(2Q22.3) WILD-TYPE	397	60.6 (6.8)

Figure S200. Get High-res Image Gene #35: 'del_2q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2q22.3' versus 'GLEASON_SCORE'

P value = 0.0947 (Wilcoxon-test), Q value = 0.21

Table S201. Gene #35: 'del_2q22.3' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 7(2Q22.3) MUTATED	84	7.8 (1.1)
DEL PEAK 7(2Q22.3) WILD-TYPE	407	7.6 (1.0)

Figure S201. Get High-res Image Gene #35: 'del_2q22.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_3p13' versus 'YEARS_TO_BIRTH'

P value = 0.0513 (Wilcoxon-test), Q value = 0.13

Table S202. Gene #36: 'del_3p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
DEL PEAK 8(3P13) MUTATED	78	59.7 (7.4)
DEL PEAK 8(3P13) WILD-TYPE	402	61.2 (6.7)

Figure S202. Get High-res Image Gene #36: 'del_3p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_3p13' versus 'RADIATION_THERAPY'

P value = 0.114 (Fisher's exact test), Q value = 0.24

Table S203. Gene #36: 'del_3p13' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 8(3P13) MUTATED	54	13
DEL PEAK 8(3P13) WILD-TYPE	324	44

Figure S203. Get High-res Image Gene #36: 'del_3p13' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_3q29' versus 'GLEASON_SCORE'

P value = 0.109 (Wilcoxon-test), Q value = 0.23

Table S204. Gene #37: 'del_3q29' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 9(3Q29) MUTATED	32	7.9 (1.1)
DEL PEAK 9(3Q29) WILD-TYPE	459	7.6 (1.0)

Figure S204. Get High-res Image Gene #37: 'del_3q29' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_4q28.2' versus 'YEARS_TO_BIRTH'

P value = 0.00158 (Wilcoxon-test), Q value = 0.0094

Table S205. Gene #38: 'del_4q28.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
DEL PEAK 10(4Q28.2) MUTATED	49	63.9 (6.0)
DEL PEAK 10(4Q28.2) WILD-TYPE	431	60.6 (6.8)

Figure S205. 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 = 0.0595 (Fisher's exact test), Q value = 0.15

Table S206. Gene #38: 'del_4q28.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 10(4Q28.2) MUTATED	15	32	3
DEL PEAK 10(4Q28.2) WILD-TYPE	173	255	7

Figure S206. Get High-res Image Gene #38: 'del_4q28.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_4q28.2' versus 'RADIATION_THERAPY'

P value = 0.11 (Fisher's exact test), Q value = 0.23

Table S207. Gene #38: 'del_4q28.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 10(4Q28.2) MUTATED	38	10
DEL PEAK 10(4Q28.2) WILD-TYPE	340	47

Figure S207. Get High-res Image Gene #38: 'del_4q28.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_4q28.2' versus 'GLEASON_SCORE'

P value = 0.000761 (Wilcoxon-test), Q value = 0.0052

Table S208. Gene #38: 'del_4q28.2' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 10(4Q28.2) MUTATED	50	8.1 (1.0)
DEL PEAK 10(4Q28.2) WILD-TYPE	441	7.6 (1.0)

Figure S208. Get High-res Image Gene #38: 'del_4q28.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_5q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.0257 (Wilcoxon-test), Q value = 0.081

Table S209. Gene #39: 'del_5q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
DEL PEAK 11(5Q11.2) MUTATED	99	62.4 (6.3)
DEL PEAK 11(5Q11.2) WILD-TYPE	381	60.6 (6.9)

Figure S209. 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 = 0.00016

Table S210. Gene #39: 'del_5q11.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 11(5Q11.2) MUTATED	16	76	5
DEL PEAK 11(5Q11.2) WILD-TYPE	172	211	5

Figure S210. 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 = 0.000371 (Fisher's exact test), Q value = 0.0032

Table S211. Gene #39: 'del_5q11.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 11(5Q11.2) MUTATED	62	29
DEL PEAK 11(5Q11.2) WILD-TYPE	280	48

Figure S211. Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_5q11.2' versus 'RADIATION_THERAPY'

P value = 0.00766 (Fisher's exact test), Q value = 0.032

Table S212. Gene #39: 'del_5q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 11(5Q11.2) MUTATED	70	20
DEL PEAK 11(5Q11.2) WILD-TYPE	308	37

Figure S212. Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_5q11.2' versus 'RESIDUAL_TUMOR'

P value = 0.0283 (Fisher's exact test), Q value = 0.086

Table S213. Gene #39: 'del_5q11.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 11(5Q11.2) MUTATED	50	39	1	4
DEL PEAK 11(5Q11.2) WILD-TYPE	262	104	4	11

Figure S213. 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 = 1.49e-05 (Wilcoxon-test), Q value = 0.00023

Table S214. Gene #39: 'del_5q11.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 11(5Q11.2) MUTATED	83	1.0 (2.2)
DEL PEAK 11(5Q11.2) WILD-TYPE	318	0.3 (1.0)

Figure S214. 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 = 5.05e-10 (Wilcoxon-test), Q value = 5.2e-08

Table S215. Gene #39: 'del_5q11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 11(5Q11.2) MUTATED	99	8.2 (1.0)
DEL PEAK 11(5Q11.2) WILD-TYPE	392	7.5 (1.0)

Figure S215. 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 = 0.00016

Table S216. Gene #40: 'del_5q13.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 12(5Q13.2) MUTATED	15	77	5
DEL PEAK 12(5Q13.2) WILD-TYPE	173	210	5

Figure S216. 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 = 0.0214 (Fisher's exact test), Q value = 0.071

Table S217. Gene #40: 'del_5q13.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 12(5Q13.2) MUTATED	67	25
DEL PEAK 12(5Q13.2) WILD-TYPE	275	52

Figure S217. Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_5q13.2' versus 'RADIATION_THERAPY'

P value = 0.0338 (Fisher's exact test), Q value = 0.097

Table S218. Gene #40: 'del_5q13.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 12(5Q13.2) MUTATED	71	18
DEL PEAK 12(5Q13.2) WILD-TYPE	307	39

Figure S218. 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 = 0.00266 (Wilcoxon-test), Q value = 0.014

Table S219. Gene #40: 'del_5q13.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 12(5Q13.2) MUTATED	84	1.0 (2.5)
DEL PEAK 12(5Q13.2) WILD-TYPE	317	0.3 (0.8)

Figure S219. 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 = 1.03e-08 (Wilcoxon-test), Q value = 6.2e-07

Table S220. Gene #40: 'del_5q13.2' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 12(5Q13.2) MUTATED	98	8.1 (1.0)
DEL PEAK 12(5Q13.2) WILD-TYPE	393	7.5 (1.0)

Figure S220. Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_5q21.1' versus 'YEARS_TO_BIRTH'

P value = 0.0567 (Wilcoxon-test), Q value = 0.14

Table S221. Gene #41: 'del_5q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
DEL PEAK 13(5Q21.1) MUTATED	107	62.1 (6.0)
DEL PEAK 13(5Q21.1) WILD-TYPE	373	60.6 (7.0)

Figure S221. 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 = 0.0258 (Fisher's exact test), Q value = 0.081

Table S222. Gene #41: 'del_5q21.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 13(5Q21.1) MUTATED	30	74	3
DEL PEAK 13(5Q21.1) WILD-TYPE	158	213	7

Figure S222. Get High-res Image Gene #41: 'del_5q21.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_5q21.1' versus 'GLEASON_SCORE'

P value = 0.00185 (Wilcoxon-test), Q value = 0.011

Table S223. Gene #41: 'del_5q21.1' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 13(5Q21.1) MUTATED	108	7.9 (1.0)
DEL PEAK 13(5Q21.1) WILD-TYPE	383	7.5 (1.0)

Figure S223. Get High-res Image Gene #41: 'del_5q21.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_5q21.1' versus 'PSA_VALUE'

P value = 0.0755 (Wilcoxon-test), Q value = 0.17

Table S224. Gene #41: 'del_5q21.1' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
DEL PEAK 13(5Q21.1) MUTATED	92	5.1 (34.0)
DEL PEAK 13(5Q21.1) WILD-TYPE	342	0.9 (3.6)

Figure S224. Get High-res Image Gene #41: 'del_5q21.1' versus Clinical Feature #10: 'PSA_VALUE'

'del_6p25.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0095 (Fisher's exact test), Q value = 0.039

Table S225. Gene #42: 'del_6p25.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 14(6P25.1) MUTATED	10	31	3
DEL PEAK 14(6P25.1) WILD-TYPE	178	256	7

Figure S225. 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 = 0.00605 (Fisher's exact test), Q value = 0.026

Table S226. Gene #42: 'del_6p25.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 14(6P25.1) MUTATED	28	15
DEL PEAK 14(6P25.1) WILD-TYPE	314	62

Figure S226. 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 = 0.00157 (Wilcoxon-test), Q value = 0.0094

Table S227. Gene #42: 'del_6p25.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 14(6P25.1) MUTATED	39	0.6 (1.0)
DEL PEAK 14(6P25.1) WILD-TYPE	362	0.4 (1.4)

Figure S227. 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 = 8.2e-06 (Wilcoxon-test), Q value = 0.00016

Table S228. Gene #42: 'del_6p25.1' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 14(6P25.1) MUTATED	46	8.2 (0.9)
DEL PEAK 14(6P25.1) WILD-TYPE	445	7.5 (1.0)

Figure S228. Get High-res Image Gene #42: 'del_6p25.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_6p25.1' versus 'RACE'

P value = 0.00664 (Fisher's exact test), Q value = 0.028

Table S229. 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 S229. Get High-res Image Gene #42: 'del_6p25.1' versus Clinical Feature #11: 'RACE'

'del_6q14.3' versus 'YEARS_TO_BIRTH'

P value = 0.00104 (Wilcoxon-test), Q value = 0.0068

Table S230. Gene #43: 'del_6q14.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
DEL PEAK 15(6Q14.3) MUTATED	175	62.3 (6.3)
DEL PEAK 15(6Q14.3) WILD-TYPE	305	60.2 (6.9)

Figure S230. 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 = 0.0666 (Fisher's exact test), Q value = 0.16

Table S231. Gene #43: 'del_6q14.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 15(6Q14.3) MUTATED	57	114	5
DEL PEAK 15(6Q14.3) WILD-TYPE	131	173	5

Figure S231. 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 = 0.0265 (Fisher's exact test), Q value = 0.082

Table S232. Gene #43: 'del_6q14.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 15(6Q14.3) MUTATED	120	38
DEL PEAK 15(6Q14.3) WILD-TYPE	222	39

Figure S232. Get High-res Image Gene #43: 'del_6q14.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_6q14.3' versus 'RESIDUAL_TUMOR'

P value = 0.00044 (Fisher's exact test), Q value = 0.0037

Table S233. Gene #43: 'del_6q14.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 15(6Q14.3) MUTATED	93	65	2	10
DEL PEAK 15(6Q14.3) WILD-TYPE	219	78	3	5

Figure S233. 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 = 0.018 (Wilcoxon-test), Q value = 0.063

Table S234. Gene #43: 'del_6q14.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 15(6Q14.3) MUTATED	152	0.5 (1.2)
DEL PEAK 15(6Q14.3) WILD-TYPE	249	0.4 (1.4)

Figure S234. 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 = 0.000445 (Wilcoxon-test), Q value = 0.0037

Table S235. Gene #43: 'del_6q14.3' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 15(6Q14.3) MUTATED	179	7.8 (1.0)
DEL PEAK 15(6Q14.3) WILD-TYPE	312	7.5 (1.0)

Figure S235. Get High-res Image Gene #43: 'del_6q14.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_7q31.33' versus 'PATHOLOGY_N_STAGE'

P value = 0.104 (Fisher's exact test), Q value = 0.22

Table S236. Gene #44: 'del_7q31.33' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 16(7Q31.33) MUTATED	17	8
DEL PEAK 16(7Q31.33) WILD-TYPE	325	69

Figure S236. Get High-res Image Gene #44: 'del_7q31.33' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_7q31.33' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.037 (Wilcoxon-test), Q value = 0.1

Table S237. Gene #44: 'del_7q31.33' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 16(7Q31.33) MUTATED	23	0.8 (1.5)
DEL PEAK 16(7Q31.33) WILD-TYPE	378	0.4 (1.4)

Figure S237. Get High-res Image Gene #44: 'del_7q31.33' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_7q31.33' versus 'GLEASON_SCORE'

P value = 0.0924 (Wilcoxon-test), Q value = 0.2

Table S238. Gene #44: 'del_7q31.33' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 16(7Q31.33) MUTATED	28	7.9 (1.1)
DEL PEAK 16(7Q31.33) WILD-TYPE	463	7.6 (1.0)

Figure S238. Get High-res Image Gene #44: 'del_7q31.33' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_8p23.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S239. Gene #45: 'del_8p23.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 17(8P23.2) MUTATED	57	158	6
DEL PEAK 17(8P23.2) WILD-TYPE	131	129	4

Figure S239. Get High-res Image Gene #45: 'del_8p23.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_8p23.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0112 (Fisher's exact test), Q value = 0.043

Table S240. Gene #45: 'del_8p23.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 17(8P23.2) MUTATED	148	46
DEL PEAK 17(8P23.2) WILD-TYPE	194	31

Figure S240. Get High-res Image Gene #45: 'del_8p23.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_8p23.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00532 (Wilcoxon-test), Q value = 0.023

Table S241. Gene #45: 'del_8p23.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 17(8P23.2) MUTATED	185	0.6 (1.6)
DEL PEAK 17(8P23.2) WILD-TYPE	216	0.3 (1.1)

Figure S241. Get High-res Image Gene #45: 'del_8p23.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_8p23.2' versus 'GLEASON_SCORE'

P value = 0.00459 (Wilcoxon-test), Q value = 0.021

Table S242. Gene #45: 'del_8p23.2' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 17(8P23.2) MUTATED	223	7.7 (1.0)
DEL PEAK 17(8P23.2) WILD-TYPE	268	7.5 (1.0)

Figure S242. Get High-res Image Gene #45: 'del_8p23.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_8p23.2' versus 'PSA_VALUE'

P value = 0.0689 (Wilcoxon-test), Q value = 0.16

Table S243. Gene #45: 'del_8p23.2' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
DEL PEAK 17(8P23.2) MUTATED	196	3.3 (23.6)
DEL PEAK 17(8P23.2) WILD-TYPE	238	0.6 (2.2)

Figure S243. Get High-res Image Gene #45: 'del_8p23.2' versus Clinical Feature #10: 'PSA_VALUE'

'del_8p21.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S244. Gene #46: 'del_8p21.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 18(8P21.3) MUTATED	81	202	8
DEL PEAK 18(8P21.3) WILD-TYPE	107	85	2

Figure S244. Get High-res Image Gene #46: 'del_8p21.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_8p21.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00272 (Fisher's exact test), Q value = 0.014

Table S245. Gene #46: 'del_8p21.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 18(8P21.3) MUTATED	198	59
DEL PEAK 18(8P21.3) WILD-TYPE	144	18

Figure S245. Get High-res Image Gene #46: 'del_8p21.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_8p21.3' versus 'RADIATION_THERAPY'

P value = 0.0589 (Fisher's exact test), Q value = 0.15

Table S246. Gene #46: 'del_8p21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 18(8P21.3) MUTATED	219	41
DEL PEAK 18(8P21.3) WILD-TYPE	159	16

Figure S246. Get High-res Image Gene #46: 'del_8p21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_8p21.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0013 (Wilcoxon-test), Q value = 0.0081

Table S247. Gene #46: 'del_8p21.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 18(8P21.3) MUTATED	245	0.6 (1.6)
DEL PEAK 18(8P21.3) WILD-TYPE	156	0.2 (0.8)

Figure S247. Get High-res Image Gene #46: 'del_8p21.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_8p21.3' versus 'GLEASON_SCORE'

P value = 0.00109 (Wilcoxon-test), Q value = 0.0071

Table S248. Gene #46: 'del_8p21.3' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 18(8P21.3) MUTATED	293	7.7 (1.0)
DEL PEAK 18(8P21.3) WILD-TYPE	198	7.4 (1.0)

Figure S248. Get High-res Image Gene #46: 'del_8p21.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_8p21.3' versus 'PSA_VALUE'

P value = 0.0838 (Wilcoxon-test), Q value = 0.19

Table S249. Gene #46: 'del_8p21.3' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
DEL PEAK 18(8P21.3) MUTATED	257	2.6 (20.6)
DEL PEAK 18(8P21.3) WILD-TYPE	177	0.7 (2.7)

Figure S249. Get High-res Image Gene #46: 'del_8p21.3' versus Clinical Feature #10: 'PSA_VALUE'

'del_9p23' versus 'PATHOLOGY_T_STAGE'

P value = 0.0238 (Fisher's exact test), Q value = 0.076

Table S250. Gene #47: 'del_9p23' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 19(9P23) MUTATED	10	33	2
DEL PEAK 19(9P23) WILD-TYPE	178	254	8

Figure S250. Get High-res Image Gene #47: 'del_9p23' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_9p23' versus 'PATHOLOGY_N_STAGE'

P value = 0.0201 (Fisher's exact test), Q value = 0.068

Table S251. Gene #47: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 19(9P23) MUTATED	29	14
DEL PEAK 19(9P23) WILD-TYPE	313	63

Figure S251. Get High-res Image Gene #47: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_9p23' versus 'RADIATION_THERAPY'

P value = 0.0963 (Fisher's exact test), Q value = 0.21

Table S252. Gene #47: 'del_9p23' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 19(9P23) MUTATED	33	9
DEL PEAK 19(9P23) WILD-TYPE	345	48

Figure S252. Get High-res Image Gene #47: 'del_9p23' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_9p23' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00755 (Wilcoxon-test), Q value = 0.032

Table S253. Gene #47: 'del_9p23' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 19(9P23) MUTATED	40	0.9 (2.0)
DEL PEAK 19(9P23) WILD-TYPE	361	0.4 (1.3)

Figure S253. Get High-res Image Gene #47: 'del_9p23' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_9p23' versus 'GLEASON_SCORE'

P value = 0.00401 (Wilcoxon-test), Q value = 0.019

Table S254. Gene #47: 'del_9p23' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 19(9P23) MUTATED	45	8.0 (1.1)
DEL PEAK 19(9P23) WILD-TYPE	446	7.6 (1.0)

Figure S254. Get High-res Image Gene #47: '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 = 0.00016

Table S255. Gene #48: 'del_10q23.31' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 20(10Q23.31) MUTATED	37	112	6
DEL PEAK 20(10Q23.31) WILD-TYPE	151	175	4

Figure S255. Get High-res Image Gene #48: 'del_10q23.31' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_10q23.31' versus 'PATHOLOGY_N_STAGE'

P value = 0.00236 (Fisher's exact test), Q value = 0.013

Table S256. Gene #48: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 20(10Q23.31) MUTATED	109	39
DEL PEAK 20(10Q23.31) WILD-TYPE	233	38

Figure S256. Get High-res Image Gene #48: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_10q23.31' versus 'RADIATION_THERAPY'

P value = 0.0214 (Fisher's exact test), Q value = 0.071

Table S257. Gene #48: 'del_10q23.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 20(10Q23.31) MUTATED	112	26
DEL PEAK 20(10Q23.31) WILD-TYPE	266	31

Figure S257. Get High-res Image Gene #48: 'del_10q23.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_10q23.31' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00118 (Wilcoxon-test), Q value = 0.0075

Table S258. Gene #48: 'del_10q23.31' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 20(10Q23.31) MUTATED	142	0.7 (1.6)
DEL PEAK 20(10Q23.31) WILD-TYPE	259	0.3 (1.2)

Figure S258. Get High-res Image Gene #48: 'del_10q23.31' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_10q23.31' versus 'GLEASON_SCORE'

P value = 5.3e-08 (Wilcoxon-test), Q value = 2.4e-06

Table S259. Gene #48: 'del_10q23.31' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 20(10Q23.31) MUTATED	156	8.0 (1.0)
DEL PEAK 20(10Q23.31) WILD-TYPE	335	7.4 (1.0)

Figure S259. Get High-res Image Gene #48: 'del_10q23.31' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_10q23.31' versus 'PSA_VALUE'

P value = 0.00956 (Wilcoxon-test), Q value = 0.039

Table S260. Gene #48: 'del_10q23.31' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
DEL PEAK 20(10Q23.31) MUTATED	140	4.3 (27.9)
DEL PEAK 20(10Q23.31) WILD-TYPE	294	0.6 (2.2)

Figure S260. Get High-res Image Gene #48: 'del_10q23.31' versus Clinical Feature #10: 'PSA_VALUE'

'del_11p11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0164 (Fisher's exact test), Q value = 0.058

Table S261. Gene #49: 'del_11p11.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 21(11P11.2) MUTATED	6	27	1
DEL PEAK 21(11P11.2) WILD-TYPE	182	260	9

Figure S261. Get High-res Image Gene #49: 'del_11p11.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_11p11.2' versus 'RESIDUAL_TUMOR'

P value = 0.043 (Fisher's exact test), Q value = 0.12

Table S262. Gene #49: 'del_11p11.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 21(11P11.2) MUTATED	15	16	0	2
DEL PEAK 21(11P11.2) WILD-TYPE	297	127	5	13

Figure S262. Get High-res Image Gene #49: 'del_11p11.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_11p11.2' versus 'GLEASON_SCORE'

P value = 0.0121 (Wilcoxon-test), Q value = 0.046

Table S263. Gene #49: 'del_11p11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 21(11P11.2) MUTATED	34	8.0 (1.0)
DEL PEAK 21(11P11.2) WILD-TYPE	457	7.6 (1.0)

Figure S263. Get High-res Image Gene #49: 'del_11p11.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_11p11.2' versus 'RACE'

P value = 0.00346 (Fisher's exact test), Q value = 0.017

Table S264. Gene #49: 'del_11p11.2' versus Clinical Feature #11: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	7	146
DEL PEAK 21(11P11.2) MUTATED	1	2	3
DEL PEAK 21(11P11.2) WILD-TYPE	1	5	143

Figure S264. Get High-res Image Gene #49: 'del_11p11.2' versus Clinical Feature #11: 'RACE'

'del_11q22.3' versus 'YEARS_TO_BIRTH'

P value = 0.0338 (Wilcoxon-test), Q value = 0.097

Table S265. Gene #50: 'del_11q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
DEL PEAK 22(11Q22.3) MUTATED	42	63.2 (6.4)
DEL PEAK 22(11Q22.3) WILD-TYPE	438	60.8 (6.8)

Figure S265. Get High-res Image Gene #50: 'del_11q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q22.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00062 (Fisher's exact test), Q value = 0.0045

Table S266. Gene #50: 'del_11q22.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 22(11Q22.3) MUTATED	7	33	3
DEL PEAK 22(11Q22.3) WILD-TYPE	181	254	7

Figure S266. Get High-res Image Gene #50: 'del_11q22.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_11q22.3' versus 'RADIATION_THERAPY'

P value = 0.0529 (Fisher's exact test), Q value = 0.14

Table S267. Gene #50: 'del_11q22.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 22(11Q22.3) MUTATED	24	8
DEL PEAK 22(11Q22.3) WILD-TYPE	354	49

Figure S267. Get High-res Image Gene #50: 'del_11q22.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_11q22.3' versus 'RESIDUAL_TUMOR'

P value = 0.00393 (Fisher's exact test), Q value = 0.019

Table S268. Gene #50: 'del_11q22.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 22(11Q22.3) MUTATED	18	23	0	0
DEL PEAK 22(11Q22.3) WILD-TYPE	294	120	5	15

Figure S268. Get High-res Image Gene #50: 'del_11q22.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_11q22.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.068 (Wilcoxon-test), Q value = 0.16

Table S269. Gene #50: 'del_11q22.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 22(11Q22.3) MUTATED	34	0.7 (1.2)
DEL PEAK 22(11Q22.3) WILD-TYPE	367	0.4 (1.4)

Figure S269. Get High-res Image Gene #50: 'del_11q22.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_11q22.3' versus 'GLEASON_SCORE'

P value = 6.89e-05 (Wilcoxon-test), Q value = 0.00086

Table S270. Gene #50: 'del_11q22.3' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 22(11Q22.3) MUTATED	43	8.2 (1.0)
DEL PEAK 22(11Q22.3) WILD-TYPE	448	7.5 (1.0)

Figure S270. Get High-res Image Gene #50: 'del_11q22.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_11q23.2' versus 'YEARS_TO_BIRTH'

P value = 0.0711 (Wilcoxon-test), Q value = 0.17

Table S271. Gene #51: 'del_11q23.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
DEL PEAK 23(11Q23.2) MUTATED	47	62.7 (6.2)
DEL PEAK 23(11Q23.2) WILD-TYPE	433	60.8 (6.9)

Figure S271. Get High-res Image Gene #51: 'del_11q23.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q23.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00264 (Fisher's exact test), Q value = 0.014

Table S272. Gene #51: 'del_11q23.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 23(11Q23.2) MUTATED	11	33	4
DEL PEAK 23(11Q23.2) WILD-TYPE	177	254	6

Figure S272. Get High-res Image Gene #51: 'del_11q23.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_11q23.2' versus 'RADIATION_THERAPY'

P value = 0.0725 (Fisher's exact test), Q value = 0.17

Table S273. Gene #51: 'del_11q23.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 23(11Q23.2) MUTATED	29	9
DEL PEAK 23(11Q23.2) WILD-TYPE	349	48

Figure S273. Get High-res Image Gene #51: 'del_11q23.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_11q23.2' versus 'RESIDUAL_TUMOR'

P value = 0.0143 (Fisher's exact test), Q value = 0.053

Table S274. Gene #51: 'del_11q23.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 23(11Q23.2) MUTATED	21	23	0	2
DEL PEAK 23(11Q23.2) WILD-TYPE	291	120	5	13

Figure S274. Get High-res Image Gene #51: 'del_11q23.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_11q23.2' versus 'GLEASON_SCORE'

P value = 8.42e-05 (Wilcoxon-test), Q value = 0.001

Table S275. Gene #51: 'del_11q23.2' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 23(11Q23.2) MUTATED	48	8.2 (1.0)
DEL PEAK 23(11Q23.2) WILD-TYPE	443	7.5 (1.0)

Figure S275. Get High-res Image Gene #51: '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 = 0.00016

Table S276. Gene #52: 'del_12p13.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 24(12P13.1) MUTATED	23	95	5
DEL PEAK 24(12P13.1) WILD-TYPE	165	192	5

Figure S276. Get High-res Image Gene #52: 'del_12p13.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_12p13.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.011 (Fisher's exact test), Q value = 0.043

Table S277. Gene #52: 'del_12p13.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 24(12P13.1) MUTATED	86	31
DEL PEAK 24(12P13.1) WILD-TYPE	256	46

Figure S277. Get High-res Image Gene #52: 'del_12p13.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_12p13.1' versus 'RADIATION_THERAPY'

P value = 0.0225 (Fisher's exact test), Q value = 0.073

Table S278. Gene #52: 'del_12p13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 24(12P13.1) MUTATED	90	22
DEL PEAK 24(12P13.1) WILD-TYPE	288	35

Figure S278. Get High-res Image Gene #52: 'del_12p13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_12p13.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00297 (Wilcoxon-test), Q value = 0.015

Table S279. Gene #52: 'del_12p13.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 24(12P13.1) MUTATED	109	0.7 (1.6)
DEL PEAK 24(12P13.1) WILD-TYPE	292	0.3 (1.3)

Figure S279. Get High-res Image Gene #52: 'del_12p13.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_12p13.1' versus 'GLEASON_SCORE'

P value = 4.49e-05 (Wilcoxon-test), Q value = 0.00061

Table S280. Gene #52: 'del_12p13.1' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 24(12P13.1) MUTATED	124	7.9 (1.0)
DEL PEAK 24(12P13.1) WILD-TYPE	367	7.5 (1.0)

Figure S280. Get High-res Image Gene #52: 'del_12p13.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_12p13.1' versus 'PSA_VALUE'

P value = 0.021 (Wilcoxon-test), Q value = 0.07

Table S281. Gene #52: 'del_12p13.1' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
DEL PEAK 24(12P13.1) MUTATED	108	1.3 (4.6)
DEL PEAK 24(12P13.1) WILD-TYPE	326	2.0 (18.3)

Figure S281. Get High-res Image Gene #52: 'del_12p13.1' versus Clinical Feature #10: 'PSA_VALUE'

'del_12q24.32' versus 'PATHOLOGY_T_STAGE'

P value = 0.00294 (Fisher's exact test), Q value = 0.015

Table S282. Gene #53: 'del_12q24.32' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 25(12Q24.32) MUTATED	7	35	1
DEL PEAK 25(12Q24.32) WILD-TYPE	181	252	9

Figure S282. Get High-res Image Gene #53: 'del_12q24.32' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_12q24.32' versus 'PATHOLOGY_N_STAGE'

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

Table S283. Gene #53: 'del_12q24.32' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 25(12Q24.32) MUTATED	27	13
DEL PEAK 25(12Q24.32) WILD-TYPE	315	64

Figure S283. Get High-res Image Gene #53: 'del_12q24.32' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_12q24.32' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0147 (Wilcoxon-test), Q value = 0.054

Table S284. Gene #53: 'del_12q24.32' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 25(12Q24.32) MUTATED	38	0.9 (2.6)
DEL PEAK 25(12Q24.32) WILD-TYPE	363	0.4 (1.2)

Figure S284. Get High-res Image Gene #53: 'del_12q24.32' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_12q24.32' versus 'GLEASON_SCORE'

P value = 0.054 (Wilcoxon-test), Q value = 0.14

Table S285. Gene #53: 'del_12q24.32' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 25(12Q24.32) MUTATED	43	7.9 (1.0)
DEL PEAK 25(12Q24.32) WILD-TYPE	448	7.6 (1.0)

Figure S285. Get High-res Image Gene #53: 'del_12q24.32' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_13q14.13' versus 'YEARS_TO_BIRTH'

P value = 0.0129 (Wilcoxon-test), Q value = 0.048

Table S286. Gene #54: 'del_13q14.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
DEL PEAK 26(13Q14.13) MUTATED	223	61.7 (6.6)
DEL PEAK 26(13Q14.13) WILD-TYPE	257	60.4 (7.0)

Figure S286. Get High-res Image Gene #54: 'del_13q14.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q14.13' versus 'PATHOLOGY_T_STAGE'

P value = 0.00433 (Fisher's exact test), Q value = 0.02

Table S287. Gene #54: 'del_13q14.13' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 26(13Q14.13) MUTATED	70	149	6
DEL PEAK 26(13Q14.13) WILD-TYPE	118	138	4

Figure S287. Get High-res Image Gene #54: 'del_13q14.13' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_13q14.13' versus 'RADIATION_THERAPY'

P value = 0.00411 (Fisher's exact test), Q value = 0.019

Table S288. Gene #54: 'del_13q14.13' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 26(13Q14.13) MUTATED	166	37
DEL PEAK 26(13Q14.13) WILD-TYPE	212	20

Figure S288. Get High-res Image Gene #54: 'del_13q14.13' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_13q14.13' versus 'RESIDUAL_TUMOR'

P value = 0.00198 (Fisher's exact test), Q value = 0.011

Table S289. Gene #54: 'del_13q14.13' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 26(13Q14.13) MUTATED	126	82	1	9
DEL PEAK 26(13Q14.13) WILD-TYPE	186	61	4	6

Figure S289. Get High-res Image Gene #54: 'del_13q14.13' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_13q14.13' versus 'GLEASON_SCORE'

P value = 1.48e-05 (Wilcoxon-test), Q value = 0.00023

Table S290. Gene #54: 'del_13q14.13' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 26(13Q14.13) MUTATED	227	7.8 (1.0)
DEL PEAK 26(13Q14.13) WILD-TYPE	264	7.4 (1.0)

Figure S290. Get High-res Image Gene #54: 'del_13q14.13' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_13q14.13' versus 'RACE'

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

Table S291. Gene #54: 'del_13q14.13' versus Clinical Feature #11: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	7	146
DEL PEAK 26(13Q14.13) MUTATED	1	7	64
DEL PEAK 26(13Q14.13) WILD-TYPE	1	0	82

Figure S291. Get High-res Image Gene #54: 'del_13q14.13' versus Clinical Feature #11: 'RACE'

'del_13q22.1' versus 'YEARS_TO_BIRTH'

P value = 0.000883 (Wilcoxon-test), Q value = 0.0059

Table S292. Gene #55: 'del_13q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
DEL PEAK 27(13Q22.1) MUTATED	173	62.3 (6.7)
DEL PEAK 27(13Q22.1) WILD-TYPE	307	60.2 (6.8)

Figure S292. Get High-res Image Gene #55: 'del_13q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q22.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00011 (Fisher's exact test), Q value = 0.0012

Table S293. Gene #55: 'del_13q22.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 27(13Q22.1) MUTATED	50	116	8
DEL PEAK 27(13Q22.1) WILD-TYPE	138	171	2

Figure S293. Get High-res Image Gene #55: 'del_13q22.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_13q22.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0927 (Fisher's exact test), Q value = 0.2

Table S294. Gene #55: 'del_13q22.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 27(13Q22.1) MUTATED	124	36
DEL PEAK 27(13Q22.1) WILD-TYPE	218	41

Figure S294. Get High-res Image Gene #55: 'del_13q22.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_13q22.1' versus 'RADIATION_THERAPY'

P value = 0.0773 (Fisher's exact test), Q value = 0.18

Table S295. Gene #55: 'del_13q22.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 27(13Q22.1) MUTATED	132	27
DEL PEAK 27(13Q22.1) WILD-TYPE	246	30

Figure S295. Get High-res Image Gene #55: 'del_13q22.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_13q22.1' versus 'RESIDUAL_TUMOR'

P value = 0.0129 (Fisher's exact test), Q value = 0.048

Table S296. Gene #55: 'del_13q22.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 27(13Q22.1) MUTATED	96	65	1	7
DEL PEAK 27(13Q22.1) WILD-TYPE	216	78	4	8

Figure S296. Get High-res Image Gene #55: 'del_13q22.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_13q22.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.037 (Wilcoxon-test), Q value = 0.1

Table S297. Gene #55: 'del_13q22.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 27(13Q22.1) MUTATED	151	0.6 (1.6)
DEL PEAK 27(13Q22.1) WILD-TYPE	250	0.3 (1.2)

Figure S297. Get High-res Image Gene #55: 'del_13q22.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_13q22.1' versus 'GLEASON_SCORE'

P value = 2.15e-10 (Wilcoxon-test), Q value = 3.1e-08

Table S298. Gene #55: 'del_13q22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 27(13Q22.1) MUTATED	176	8.0 (1.0)
DEL PEAK 27(13Q22.1) WILD-TYPE	315	7.4 (1.0)

Figure S298. Get High-res Image Gene #55: 'del_13q22.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_13q22.1' versus 'RACE'

P value = 0.00047 (Fisher's exact test), Q value = 0.0038

Table S299. Gene #55: 'del_13q22.1' versus Clinical Feature #11: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	7	146
DEL PEAK 27(13Q22.1) MUTATED	0	7	51
DEL PEAK 27(13Q22.1) WILD-TYPE	2	0	95

Figure S299. Get High-res Image Gene #55: '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 = 0.00016

Table S300. Gene #56: 'del_15q21.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 28(15Q21.3) MUTATED	9	53	4
DEL PEAK 28(15Q21.3) WILD-TYPE	179	234	6

Figure S300. Get High-res Image Gene #56: 'del_15q21.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_15q21.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00155 (Fisher's exact test), Q value = 0.0094

Table S301. Gene #56: 'del_15q21.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 28(15Q21.3) MUTATED	38	20
DEL PEAK 28(15Q21.3) WILD-TYPE	304	57

Figure S301. Get High-res Image Gene #56: 'del_15q21.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_15q21.3' versus 'RADIATION_THERAPY'

P value = 0.00261 (Fisher's exact test), Q value = 0.014

Table S302. Gene #56: 'del_15q21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 28(15Q21.3) MUTATED	41	15
DEL PEAK 28(15Q21.3) WILD-TYPE	337	42

Figure S302. Get High-res Image Gene #56: 'del_15q21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_15q21.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000614 (Wilcoxon-test), Q value = 0.0045

Table S303. Gene #56: 'del_15q21.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 28(15Q21.3) MUTATED	57	0.8 (1.4)
DEL PEAK 28(15Q21.3) WILD-TYPE	344	0.4 (1.3)

Figure S303. Get High-res Image Gene #56: 'del_15q21.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_15q21.3' versus 'GLEASON_SCORE'

P value = 1.73e-08 (Wilcoxon-test), Q value = 8.8e-07

Table S304. Gene #56: 'del_15q21.3' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 28(15Q21.3) MUTATED	66	8.3 (1.0)
DEL PEAK 28(15Q21.3) WILD-TYPE	425	7.5 (1.0)

Figure S304. Get High-res Image Gene #56: 'del_15q21.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_15q21.3' versus 'PSA_VALUE'

P value = 0.112 (Wilcoxon-test), Q value = 0.23

Table S305. Gene #56: 'del_15q21.3' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
DEL PEAK 28(15Q21.3) MUTATED	52	2.0 (5.9)
DEL PEAK 28(15Q21.3) WILD-TYPE	382	1.8 (16.9)

Figure S305. Get High-res Image Gene #56: 'del_15q21.3' versus Clinical Feature #10: 'PSA_VALUE'

'del_16q22.3' versus 'YEARS_TO_BIRTH'

P value = 0.0415 (Wilcoxon-test), Q value = 0.11

Table S306. Gene #57: 'del_16q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
DEL PEAK 29(16Q22.3) MUTATED	186	61.7 (6.6)
DEL PEAK 29(16Q22.3) WILD-TYPE	294	60.5 (6.9)

Figure S306. Get High-res Image Gene #57: 'del_16q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q22.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00022 (Fisher's exact test), Q value = 0.0022

Table S307. Gene #57: 'del_16q22.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 29(16Q22.3) MUTATED	53	129	6
DEL PEAK 29(16Q22.3) WILD-TYPE	135	158	4

Figure S307. Get High-res Image Gene #57: 'del_16q22.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_16q22.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0289 (Fisher's exact test), Q value = 0.087

Table S308. Gene #57: 'del_16q22.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 29(16Q22.3) MUTATED	130	40
DEL PEAK 29(16Q22.3) WILD-TYPE	212	37

Figure S308. Get High-res Image Gene #57: 'del_16q22.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_16q22.3' versus 'RESIDUAL_TUMOR'

P value = 0.0324 (Fisher's exact test), Q value = 0.094

Table S309. Gene #57: 'del_16q22.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 29(16Q22.3) MUTATED	108	69	1	5
DEL PEAK 29(16Q22.3) WILD-TYPE	204	74	4	10

Figure S309. Get High-res Image Gene #57: 'del_16q22.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_16q22.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0106 (Wilcoxon-test), Q value = 0.042

Table S310. Gene #57: 'del_16q22.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 29(16Q22.3) MUTATED	161	0.6 (1.7)
DEL PEAK 29(16Q22.3) WILD-TYPE	240	0.3 (1.0)

Figure S310. Get High-res Image Gene #57: 'del_16q22.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_16q22.3' versus 'GLEASON_SCORE'

P value = 7.22e-09 (Wilcoxon-test), Q value = 4.7e-07

Table S311. Gene #57: 'del_16q22.3' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 29(16Q22.3) MUTATED	190	7.9 (1.0)
DEL PEAK 29(16Q22.3) WILD-TYPE	301	7.4 (1.0)

Figure S311. Get High-res Image Gene #57: 'del_16q22.3' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_16q22.3' versus 'PSA_VALUE'

P value = 0.0905 (Wilcoxon-test), Q value = 0.2

Table S312. Gene #57: 'del_16q22.3' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
DEL PEAK 29(16Q22.3) MUTATED	163	1.5 (4.9)
DEL PEAK 29(16Q22.3) WILD-TYPE	271	2.0 (19.9)

Figure S312. Get High-res Image Gene #57: 'del_16q22.3' versus Clinical Feature #10: 'PSA_VALUE'

'del_16q24.1' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00029

Table S313. Gene #58: 'del_16q24.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 30(16Q24.1) MUTATED	56	147	6
DEL PEAK 30(16Q24.1) WILD-TYPE	132	140	4

Figure S313. Get High-res Image Gene #58: 'del_16q24.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_16q24.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0425 (Fisher's exact test), Q value = 0.12

Table S314. Gene #58: 'del_16q24.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 30(16Q24.1) MUTATED	146	43
DEL PEAK 30(16Q24.1) WILD-TYPE	196	34

Figure S314. Get High-res Image Gene #58: 'del_16q24.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_16q24.1' versus 'RESIDUAL_TUMOR'

P value = 0.119 (Fisher's exact test), Q value = 0.24

Table S315. Gene #58: 'del_16q24.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 30(16Q24.1) MUTATED	124	73	2	5
DEL PEAK 30(16Q24.1) WILD-TYPE	188	70	3	10

Figure S315. Get High-res Image Gene #58: 'del_16q24.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_16q24.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0209 (Wilcoxon-test), Q value = 0.07

Table S316. Gene #58: 'del_16q24.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 30(16Q24.1) MUTATED	181	0.6 (1.8)
DEL PEAK 30(16Q24.1) WILD-TYPE	220	0.3 (0.8)

Figure S316. Get High-res Image Gene #58: 'del_16q24.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_16q24.1' versus 'GLEASON_SCORE'

P value = 3.01e-09 (Wilcoxon-test), Q value = 2.1e-07

Table S317. Gene #58: 'del_16q24.1' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 30(16Q24.1) MUTATED	212	7.9 (1.0)
DEL PEAK 30(16Q24.1) WILD-TYPE	279	7.4 (0.9)

Figure S317. Get High-res Image Gene #58: 'del_16q24.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_16q24.1' versus 'PSA_VALUE'

P value = 0.0634 (Wilcoxon-test), Q value = 0.15

Table S318. Gene #58: 'del_16q24.1' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
DEL PEAK 30(16Q24.1) MUTATED	184	3.4 (24.2)
DEL PEAK 30(16Q24.1) WILD-TYPE	250	0.6 (3.0)

Figure S318. Get High-res Image Gene #58: '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 = 0.00016

Table S319. Gene #59: 'del_17p13.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 31(17P13.1) MUTATED	39	114	6
DEL PEAK 31(17P13.1) WILD-TYPE	149	173	4

Figure S319. Get High-res Image Gene #59: 'del_17p13.1' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_17p13.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00344 (Fisher's exact test), Q value = 0.017

Table S320. Gene #59: 'del_17p13.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 31(17P13.1) MUTATED	107	38
DEL PEAK 31(17P13.1) WILD-TYPE	235	39

Figure S320. Get High-res Image Gene #59: 'del_17p13.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_17p13.1' versus 'RADIATION_THERAPY'

P value = 0.0161 (Fisher's exact test), Q value = 0.058

Table S321. Gene #59: 'del_17p13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 31(17P13.1) MUTATED	117	27
DEL PEAK 31(17P13.1) WILD-TYPE	261	30

Figure S321. Get High-res Image Gene #59: 'del_17p13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_17p13.1' versus 'RESIDUAL_TUMOR'

P value = 0.0152 (Fisher's exact test), Q value = 0.055

Table S322. Gene #59: 'del_17p13.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 31(17P13.1) MUTATED	92	61	0	4
DEL PEAK 31(17P13.1) WILD-TYPE	220	82	5	11

Figure S322. Get High-res Image Gene #59: 'del_17p13.1' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_17p13.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000435 (Wilcoxon-test), Q value = 0.0037

Table S323. Gene #59: 'del_17p13.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 31(17P13.1) MUTATED	135	0.7 (1.7)
DEL PEAK 31(17P13.1) WILD-TYPE	266	0.3 (1.2)

Figure S323. Get High-res Image Gene #59: 'del_17p13.1' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_17p13.1' versus 'GLEASON_SCORE'

P value = 1.99e-09 (Wilcoxon-test), Q value = 1.7e-07

Table S324. Gene #59: 'del_17p13.1' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 31(17P13.1) MUTATED	162	8.0 (1.0)
DEL PEAK 31(17P13.1) WILD-TYPE	329	7.4 (0.9)

Figure S324. Get High-res Image Gene #59: 'del_17p13.1' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_17q21.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.114 (Fisher's exact test), Q value = 0.24

Table S325. Gene #60: 'del_17q21.31' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 32(17Q21.31) MUTATED	29	63	3
DEL PEAK 32(17Q21.31) WILD-TYPE	159	224	7

Figure S325. Get High-res Image Gene #60: 'del_17q21.31' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_18q21.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.00045 (Fisher's exact test), Q value = 0.0037

Table S326. Gene #61: 'del_18q21.31' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 33(18Q21.31) MUTATED	32	92	4
DEL PEAK 33(18Q21.31) WILD-TYPE	156	195	6

Figure S326. Get High-res Image Gene #61: 'del_18q21.31' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_18q21.31' versus 'PATHOLOGY_N_STAGE'

P value = 0.0239 (Fisher's exact test), Q value = 0.076

Table S327. Gene #61: 'del_18q21.31' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 33(18Q21.31) MUTATED	87	30
DEL PEAK 33(18Q21.31) WILD-TYPE	255	47

Figure S327. Get High-res Image Gene #61: 'del_18q21.31' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_18q21.31' versus 'RADIATION_THERAPY'

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

Table S328. Gene #61: 'del_18q21.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 33(18Q21.31) MUTATED	91	21
DEL PEAK 33(18Q21.31) WILD-TYPE	287	36

Figure S328. Get High-res Image Gene #61: 'del_18q21.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_18q21.31' versus 'RESIDUAL_TUMOR'

P value = 0.00116 (Fisher's exact test), Q value = 0.0074

Table S329. Gene #61: 'del_18q21.31' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 33(18Q21.31) MUTATED	70	55	0	2
DEL PEAK 33(18Q21.31) WILD-TYPE	242	88	5	13

Figure S329. Get High-res Image Gene #61: 'del_18q21.31' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_18q21.31' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0142 (Wilcoxon-test), Q value = 0.052

Table S330. Gene #61: 'del_18q21.31' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 33(18Q21.31) MUTATED	112	0.7 (2.1)
DEL PEAK 33(18Q21.31) WILD-TYPE	289	0.3 (1.0)

Figure S330. Get High-res Image Gene #61: 'del_18q21.31' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_18q21.31' versus 'GLEASON_SCORE'

P value = 4.75e-06 (Wilcoxon-test), Q value = 0.00013

Table S331. Gene #61: 'del_18q21.31' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 33(18Q21.31) MUTATED	130	8.0 (1.0)
DEL PEAK 33(18Q21.31) WILD-TYPE	361	7.5 (1.0)

Figure S331. Get High-res Image Gene #61: 'del_18q21.31' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_18q23' versus 'PATHOLOGY_T_STAGE'

P value = 5e-04 (Fisher's exact test), Q value = 0.0038

Table S332. Gene #62: 'del_18q23' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 34(18Q23) MUTATED	34	96	4
DEL PEAK 34(18Q23) WILD-TYPE	154	191	6

Figure S332. Get High-res Image Gene #62: 'del_18q23' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_18q23' versus 'PATHOLOGY_N_STAGE'

P value = 0.00519 (Fisher's exact test), Q value = 0.023

Table S333. Gene #62: 'del_18q23' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 34(18Q23) MUTATED	89	33
DEL PEAK 34(18Q23) WILD-TYPE	253	44

Figure S333. Get High-res Image Gene #62: 'del_18q23' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_18q23' versus 'RADIATION_THERAPY'

P value = 0.11 (Fisher's exact test), Q value = 0.23

Table S334. Gene #62: 'del_18q23' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 34(18Q23) MUTATED	98	21
DEL PEAK 34(18Q23) WILD-TYPE	280	36

Figure S334. Get High-res Image Gene #62: 'del_18q23' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_18q23' versus 'RESIDUAL_TUMOR'

P value = 0.0037 (Fisher's exact test), Q value = 0.018

Table S335. Gene #62: 'del_18q23' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 34(18Q23) MUTATED	75	55	0	2
DEL PEAK 34(18Q23) WILD-TYPE	237	88	5	13

Figure S335. Get High-res Image Gene #62: 'del_18q23' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_18q23' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00234 (Wilcoxon-test), Q value = 0.013

Table S336. Gene #62: 'del_18q23' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 34(18Q23) MUTATED	117	0.8 (2.1)
DEL PEAK 34(18Q23) WILD-TYPE	284	0.3 (0.9)

Figure S336. Get High-res Image Gene #62: 'del_18q23' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_18q23' versus 'GLEASON_SCORE'

P value = 9.81e-07 (Wilcoxon-test), Q value = 3.2e-05

Table S337. Gene #62: 'del_18q23' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 34(18Q23) MUTATED	136	8.0 (1.0)
DEL PEAK 34(18Q23) WILD-TYPE	355	7.5 (1.0)

Figure S337. Get High-res Image Gene #62: 'del_18q23' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_18q23' versus 'PSA_VALUE'

P value = 0.033 (Wilcoxon-test), Q value = 0.095

Table S338. Gene #62: 'del_18q23' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
DEL PEAK 34(18Q23) MUTATED	119	4.3 (30.0)
DEL PEAK 34(18Q23) WILD-TYPE	315	0.9 (3.4)

Figure S338. Get High-res Image Gene #62: 'del_18q23' versus Clinical Feature #10: 'PSA_VALUE'

'del_19q13.2' versus 'Time to Death'

P value = 0.109 (logrank test), Q value = 0.23

Table S339. Gene #63: 'del_19q13.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	489	9	0.7 - 165.2 (28.8)
DEL PEAK 35(19Q13.2) MUTATED	52	2	0.8 - 113.3 (28.8)
DEL PEAK 35(19Q13.2) WILD-TYPE	437	7	0.7 - 165.2 (28.8)

Figure S339. Get High-res Image Gene #63: 'del_19q13.2' versus Clinical Feature #1: 'Time to Death'

'del_19q13.2' versus 'YEARS_TO_BIRTH'

P value = 0.0496 (Wilcoxon-test), Q value = 0.13

Table S340. Gene #63: 'del_19q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
DEL PEAK 35(19Q13.2) MUTATED	51	62.6 (6.6)
DEL PEAK 35(19Q13.2) WILD-TYPE	429	60.8 (6.8)

Figure S340. Get High-res Image Gene #63: 'del_19q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19q13.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00499 (Fisher's exact test), Q value = 0.022

Table S341. Gene #63: 'del_19q13.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 35(19Q13.2) MUTATED	11	37	3
DEL PEAK 35(19Q13.2) WILD-TYPE	177	250	7

Figure S341. Get High-res Image Gene #63: 'del_19q13.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_19q13.2' versus 'RESIDUAL_TUMOR'

P value = 0.0428 (Fisher's exact test), Q value = 0.12

Table S342. Gene #63: 'del_19q13.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
DEL PEAK 35(19Q13.2) MUTATED	27	24	0	0
DEL PEAK 35(19Q13.2) WILD-TYPE	285	119	5	15

Figure S342. Get High-res Image Gene #63: 'del_19q13.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_19q13.2' versus 'GLEASON_SCORE'

P value = 0.00025 (Wilcoxon-test), Q value = 0.0024

Table S343. Gene #63: 'del_19q13.2' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 35(19Q13.2) MUTATED	52	8.1 (1.0)
DEL PEAK 35(19Q13.2) WILD-TYPE	439	7.5 (1.0)

Figure S343. Get High-res Image Gene #63: 'del_19q13.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_21q22.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00166 (Fisher's exact test), Q value = 0.0098

Table S344. Gene #64: 'del_21q22.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 36(21Q22.2) MUTATED	10	39	3
DEL PEAK 36(21Q22.2) WILD-TYPE	178	248	7

Figure S344. Get High-res Image Gene #64: 'del_21q22.2' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_21q22.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.066 (Fisher's exact test), Q value = 0.16

Table S345. Gene #64: 'del_21q22.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
DEL PEAK 36(21Q22.2) MUTATED	32	13
DEL PEAK 36(21Q22.2) WILD-TYPE	310	64

Figure S345. Get High-res Image Gene #64: 'del_21q22.2' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_21q22.2' versus 'RADIATION_THERAPY'

P value = 0.101 (Fisher's exact test), Q value = 0.22

Table S346. Gene #64: 'del_21q22.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
DEL PEAK 36(21Q22.2) MUTATED	36	10
DEL PEAK 36(21Q22.2) WILD-TYPE	342	47

Figure S346. Get High-res Image Gene #64: 'del_21q22.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_21q22.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0341 (Wilcoxon-test), Q value = 0.097

Table S347. Gene #64: 'del_21q22.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 36(21Q22.2) MUTATED	42	0.8 (1.9)
DEL PEAK 36(21Q22.2) WILD-TYPE	359	0.4 (1.3)

Figure S347. Get High-res Image Gene #64: 'del_21q22.2' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'del_21q22.2' versus 'GLEASON_SCORE'

P value = 0.0347 (Wilcoxon-test), Q value = 0.098

Table S348. Gene #64: 'del_21q22.2' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
DEL PEAK 36(21Q22.2) MUTATED	52	7.9 (1.1)
DEL PEAK 36(21Q22.2) WILD-TYPE	439	7.6 (1.0)

Figure S348. Get High-res Image Gene #64: 'del_21q22.2' versus Clinical Feature #9: 'GLEASON_SCORE'

'del_21q22.2' versus 'RACE'

P value = 0.0774 (Fisher's exact test), Q value = 0.18

Table S349. Gene #64: 'del_21q22.2' versus Clinical Feature #11: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	7	146
DEL PEAK 36(21Q22.2) MUTATED	1	2	15
DEL PEAK 36(21Q22.2) WILD-TYPE	1	5	131

Figure S349. Get High-res Image Gene #64: 'del_21q22.2' versus Clinical Feature #11: 'RACE'

'del_21q22.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0509 (Fisher's exact test), Q value = 0.13

Table S350. Gene #65: 'del_21q22.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
DEL PEAK 37(21Q22.3) MUTATED	46	94	5
DEL PEAK 37(21Q22.3) WILD-TYPE	142	193	5

Figure S350. Get High-res Image Gene #65: 'del_21q22.3' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'del_21q22.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0572 (Wilcoxon-test), Q value = 0.14

Table S351. Gene #65: 'del_21q22.3' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
DEL PEAK 37(21Q22.3) MUTATED	119	0.7 (2.0)
DEL PEAK 37(21Q22.3) WILD-TYPE	282	0.3 (1.0)

Figure S351. Get High-res Image Gene #65: '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/19782426/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PRAD-TP/19775467/PRAD-TP.merged_data.txt
Number of patients = 491
Number of significantly focal cnvs = 65
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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