Prostate Adenocarcinoma: Correlation between copy number variation genes and molecular subtypes<BR>(primary solid tumor cohort)

Prostate Adenocarcinoma: Correlation between copy number variation genes and molecular subtypes
(primary solid tumor cohort)

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

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 47 peak regions and 6 molecular subtypes across 187 patients, 49 significant findings detected with Q value < 0.25.

Amp Peak 2(3q26.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 3(7p15.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 4(7q34) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 5(8p11.22) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(8q21.13) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(11q13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p31.3) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 5(2q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 8(4q28.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 9(5q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 10(5q21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 11(6q15) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 13(8p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 14(8p11.21) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 15(9p22.3) cnvs correlated to 'CN_CNMF'.
Del Peak 16(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 18(12p13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 19(13q14.13) cnvs correlated to 'CN_CNMF'.
Del Peak 20(16q24.1) cnvs correlated to 'CN_CNMF'.
Del Peak 21(17p13.1) cnvs correlated to 'CN_CNMF'.
Del Peak 22(17q21.31) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 23(18q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 24(18q23) cnvs correlated to 'CN_CNMF'.
Del Peak 25(21q22.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 26(21q22.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 47 regions and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 49 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 11(6q15)	59 (32%)	128	2.58e-18 (7.29e-16)	8.94e-12 (2.47e-09)	1.13e-06 (0.000298)	3.91e-05 (0.00989)	0.000276 (0.0669)	0.824 (1.00)
Del Peak 26(21q22 3)	60 (32%)	127	1.77e-06 (0.000463)	5.56e-13 (1.55e-10)	9.24e-11 (2.53e-08)	8.05e-13 (2.24e-10)	0.0567 (1.00)	0.00017 (0.0417)
Del Peak 13(8p21 3)	108 (58%)	79	1.68e-08 (4.51e-06)	2.8e-06 (0.000725)	6.83e-05 (0.0171)	0.000164 (0.0406)	0.00184 (0.418)	0.0562 (1.00)
Del Peak 16(10q23 31)	65 (35%)	122	7.27e-07 (0.000193)	3.01e-06 (0.000776)	4.72e-08 (1.26e-05)	1e-06 (0.000265)	0.0408 (1.00)	0.0472 (1.00)
Del Peak 25(21q22 2)	61 (33%)	126	1.94e-06 (0.000507)	7.96e-14 (2.23e-11)	6.59e-10 (1.79e-07)	1.91e-12 (5.29e-10)	0.138 (1.00)	0.00284 (0.64)
Del Peak 22(17q21 31)	36 (19%)	151	0.00697 (1.00)	3.14e-05 (0.00799)	2.6e-05 (0.00663)	5.54e-05 (0.014)	0.484 (1.00)	0.289 (1.00)
Amp Peak 4(7q34)	32 (17%)	155	0.000158 (0.0393)	0.00441 (0.961)	0.00179 (0.409)	0.000969 (0.228)	0.85 (1.00)	0.893 (1.00)
Del Peak 8(4q28 2)	17 (9%)	170	0.000215 (0.0526)	0.000189 (0.0464)	0.0149 (1.00)	0.0943 (1.00)	0.381 (1.00)	0.0663 (1.00)
Del Peak 9(5q11 2)	30 (16%)	157	2.63e-07 (7e-05)	0.00098 (0.229)	0.0901 (1.00)	0.0433 (1.00)	0.269 (1.00)	0.701 (1.00)
Del Peak 10(5q21 1)	33 (18%)	154	9.42e-12 (2.59e-09)	2.77e-06 (0.00072)	0.00269 (0.608)	0.00737 (1.00)	0.299 (1.00)	0.538 (1.00)
Del Peak 14(8p11 21)	59 (32%)	128	0.0124 (1.00)	0.000234 (0.0569)	0.000913 (0.216)	0.0164 (1.00)	0.281 (1.00)	0.207 (1.00)
Amp Peak 2(3q26 2)	27 (14%)	160	0.0003 (0.0722)	0.0796 (1.00)	0.305 (1.00)	0.495 (1.00)	0.841 (1.00)	0.343 (1.00)
Amp Peak 3(7p15 3)	35 (19%)	152	3.5e-06 (0.000898)	0.0521 (1.00)	0.00785 (1.00)	0.0135 (1.00)	0.87 (1.00)	0.55 (1.00)
Amp Peak 5(8p11 22)	17 (9%)	170	1.44e-05 (0.00367)	0.263 (1.00)	0.0508 (1.00)	0.268 (1.00)	0.587 (1.00)	0.454 (1.00)
Amp Peak 6(8q21 13)	46 (25%)	141	4.82e-10 (1.31e-07)	0.00429 (0.939)	0.00137 (0.32)	0.00784 (1.00)	0.372 (1.00)	0.313 (1.00)
Amp Peak 7(11q13 2)	11 (6%)	176	0.000495 (0.118)	0.304 (1.00)	0.193 (1.00)	0.355 (1.00)	0.895 (1.00)	0.589 (1.00)
Del Peak 1(1p31 3)	22 (12%)	165	0.0439 (1.00)	0.000722 (0.171)	0.00169 (0.39)	0.00458 (0.993)	0.187 (1.00)	0.152 (1.00)
Del Peak 5(2q22 1)	22 (12%)	165	6.01e-05 (0.0151)	0.0015 (0.346)	0.11 (1.00)	0.033 (1.00)	0.0121 (1.00)	0.00772 (1.00)
Del Peak 15(9p22 3)	15 (8%)	172	0.000599 (0.143)	0.326 (1.00)	0.216 (1.00)	0.268 (1.00)	0.642 (1.00)	1 (1.00)
Del Peak 18(12p13 2)	39 (21%)	148	7.1e-05 (0.0177)	0.00669 (1.00)	0.562 (1.00)	0.0963 (1.00)	0.0527 (1.00)	0.856 (1.00)
Del Peak 19(13q14 13)	83 (44%)	104	0.00032 (0.0767)	0.00348 (0.776)	0.00147 (0.341)	0.00478 (1.00)	0.306 (1.00)	0.363 (1.00)
Del Peak 20(16q24 1)	74 (40%)	113	3.33e-10 (9.08e-08)	0.0036 (0.8)	0.0228 (1.00)	0.0158 (1.00)	0.0117 (1.00)	0.0121 (1.00)
Del Peak 21(17p13 1)	46 (25%)	141	2.13e-09 (5.73e-07)	0.131 (1.00)	0.0284 (1.00)	0.00411 (0.904)	0.336 (1.00)	0.0521 (1.00)
Del Peak 23(18q22 1)	46 (25%)	141	7.86e-10 (2.12e-07)	0.621 (1.00)	0.196 (1.00)	0.449 (1.00)	0.0534 (1.00)	0.152 (1.00)
Del Peak 24(18q23)	52 (28%)	135	7.39e-14 (2.08e-11)	0.411 (1.00)	0.0654 (1.00)	0.136 (1.00)	0.104 (1.00)	0.447 (1.00)
Amp Peak 1(1q21 3)	12 (6%)	175	0.0143 (1.00)	0.214 (1.00)	0.144 (1.00)	0.124 (1.00)	0.0442 (1.00)	0.919 (1.00)
Amp Peak 8(12q24 32)	7 (4%)	180	0.00207 (0.471)	0.263 (1.00)	0.894 (1.00)	0.183 (1.00)	0.456 (1.00)	0.864 (1.00)
Amp Peak 9(14q21 1)	10 (5%)	177	0.0333 (1.00)	0.145 (1.00)	0.00905 (1.00)	0.518 (1.00)	0.615 (1.00)	0.0874 (1.00)
Amp Peak 10(20q13 33)	12 (6%)	175	0.00575 (1.00)	0.00344 (0.771)	0.0118 (1.00)	0.00956 (1.00)	0.29 (1.00)	0.13 (1.00)
Amp Peak 11(21q21 3)	7 (4%)	180	0.0323 (1.00)	0.208 (1.00)	0.218 (1.00)	0.288 (1.00)	0.844 (1.00)	0.181 (1.00)
Amp Peak 12(Xp22 11)	5 (3%)	182	0.363 (1.00)	1 (1.00)	0.74 (1.00)	0.606 (1.00)	0.21 (1.00)	0.396 (1.00)
Amp Peak 13(Xp22 11)	5 (3%)	182	0.726 (1.00)	0.613 (1.00)	1 (1.00)	0.735 (1.00)	0.755 (1.00)	0.325 (1.00)
Amp Peak 14(Xp21 1)	4 (2%)	183	0.68 (1.00)	0.389 (1.00)	1 (1.00)	1 (1.00)	0.266 (1.00)	0.666 (1.00)
Amp Peak 15(Xq12)	4 (2%)	183	0.278 (1.00)	0.182 (1.00)	0.0637 (1.00)	0.021 (1.00)	0.603 (1.00)	0.393 (1.00)
Amp Peak 16(Xq21 1)	7 (4%)	180	0.39 (1.00)	0.208 (1.00)	0.199 (1.00)	0.234 (1.00)	0.406 (1.00)	0.771 (1.00)
Amp Peak 17(Xq21 1)	5 (3%)	182	0.363 (1.00)	0.00385 (0.852)	0.529 (1.00)	0.332 (1.00)	0.869 (1.00)	0.845 (1.00)
Amp Peak 18(Xq21 31)	5 (3%)	182	0.139 (1.00)	0.275 (1.00)	0.325 (1.00)	0.138 (1.00)	0.703 (1.00)	1 (1.00)
Amp Peak 19(Xq25)	4 (2%)	183	0.0497 (1.00)	0.226 (1.00)	0.391 (1.00)	0.173 (1.00)	0.404 (1.00)	0.133 (1.00)
Amp Peak 20(Xq25)	6 (3%)	181	1 (1.00)	0.252 (1.00)	0.118 (1.00)	0.5 (1.00)	0.197 (1.00)	0.405 (1.00)
Amp Peak 21(Xq27 1)	9 (5%)	178	0.00666 (1.00)	0.396 (1.00)	0.835 (1.00)	0.831 (1.00)	0.0648 (1.00)	0.0234 (1.00)
Del Peak 2(1p21 3)	16 (9%)	171	0.00945 (1.00)	0.643 (1.00)	0.945 (1.00)	1 (1.00)	0.101 (1.00)	0.942 (1.00)
Del Peak 3(1q23 1)	8 (4%)	179	0.096 (1.00)	0.16 (1.00)	0.136 (1.00)	0.111 (1.00)	0.0579 (1.00)	0.707 (1.00)
Del Peak 4(1q42 13)	18 (10%)	169	0.448 (1.00)	0.00603 (1.00)	0.73 (1.00)	0.807 (1.00)	0.27 (1.00)	0.791 (1.00)
Del Peak 6(3p13)	28 (15%)	159	0.668 (1.00)	0.0261 (1.00)	0.294 (1.00)	0.0302 (1.00)	0.195 (1.00)	0.117 (1.00)
Del Peak 7(3q29)	12 (6%)	175	0.768 (1.00)	0.0594 (1.00)	0.0694 (1.00)	0.0229 (1.00)	0.579 (1.00)	1 (1.00)
Del Peak 12(7q36 1)	9 (5%)	178	0.382 (1.00)	0.754 (1.00)	0.596 (1.00)	0.483 (1.00)	0.69 (1.00)	0.564 (1.00)
Del Peak 17(11q23 2)	23 (12%)	164	0.0629 (1.00)	0.223 (1.00)	0.877 (1.00)	0.916 (1.00)	0.338 (1.00)	0.348 (1.00)

'Amp Peak 2(3q26.2) mutation analysis' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.072

Table S1. Gene #2: 'Amp Peak 2(3q26.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
AMP PEAK 2(3Q26.2) MUTATED	7	4	16	0
AMP PEAK 2(3Q26.2) WILD-TYPE	27	88	43	2

Figure S1. Get High-res Image Gene #2: 'Amp Peak 2(3q26.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 3(7p15.3) mutation analysis' versus 'CN_CNMF'

P value = 3.5e-06 (Fisher's exact test), Q value = 9e-04

Table S2. Gene #3: 'Amp Peak 3(7p15.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
AMP PEAK 3(7P15.3) MUTATED	5	6	23	1
AMP PEAK 3(7P15.3) WILD-TYPE	29	86	36	1

Figure S2. Get High-res Image Gene #3: 'Amp Peak 3(7p15.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 4(7q34) mutation analysis' versus 'CN_CNMF'

P value = 0.000158 (Fisher's exact test), Q value = 0.039

Table S3. Gene #4: 'Amp Peak 4(7q34) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
AMP PEAK 4(7Q34) MUTATED	6	6	19	1
AMP PEAK 4(7Q34) WILD-TYPE	28	86	40	1

Figure S3. Get High-res Image Gene #4: 'Amp Peak 4(7q34) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 4(7q34) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000969 (Fisher's exact test), Q value = 0.23

Table S4. Gene #4: 'Amp Peak 4(7q34) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	75	51
AMP PEAK 4(7Q34) MUTATED	17	9	4
AMP PEAK 4(7Q34) WILD-TYPE	32	66	47

Figure S4. Get High-res Image Gene #4: 'Amp Peak 4(7q34) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 5(8p11.22) mutation analysis' versus 'CN_CNMF'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.0037

Table S5. Gene #5: 'Amp Peak 5(8p11.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
AMP PEAK 5(8P11.22) MUTATED	2	1	13	1
AMP PEAK 5(8P11.22) WILD-TYPE	32	91	46	1

Figure S5. Get High-res Image Gene #5: 'Amp Peak 5(8p11.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 6(8q21.13) mutation analysis' versus 'CN_CNMF'

P value = 4.82e-10 (Fisher's exact test), Q value = 1.3e-07

Table S6. Gene #6: 'Amp Peak 6(8q21.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
AMP PEAK 6(8Q21.13) MUTATED	6	7	32	1
AMP PEAK 6(8Q21.13) WILD-TYPE	28	85	27	1

Figure S6. Get High-res Image Gene #6: 'Amp Peak 6(8q21.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 7(11q13.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000495 (Fisher's exact test), Q value = 0.12

Table S7. Gene #7: 'Amp Peak 7(11q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
AMP PEAK 7(11Q13.2) MUTATED	0	1	10	0
AMP PEAK 7(11Q13.2) WILD-TYPE	34	91	49	2

Figure S7. Get High-res Image Gene #7: 'Amp Peak 7(11q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 1(1p31.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000722 (Fisher's exact test), Q value = 0.17

Table S8. Gene #22: 'Del Peak 1(1p31.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	77	55
DEL PEAK 1(1P31.3) MUTATED	4	17	1
DEL PEAK 1(1P31.3) WILD-TYPE	51	60	54

Figure S8. Get High-res Image Gene #22: 'Del Peak 1(1p31.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 5(2q22.1) mutation analysis' versus 'CN_CNMF'

P value = 6.01e-05 (Fisher's exact test), Q value = 0.015

Table S9. Gene #26: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 5(2Q22.1) MUTATED	8	2	11	1
DEL PEAK 5(2Q22.1) WILD-TYPE	26	90	48	1

Figure S9. Get High-res Image Gene #26: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 8(4q28.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000215 (Fisher's exact test), Q value = 0.053

Table S10. Gene #29: 'Del Peak 8(4q28.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 8(4Q28.2) MUTATED	4	1	12	0
DEL PEAK 8(4Q28.2) WILD-TYPE	30	91	47	2

Figure S10. Get High-res Image Gene #29: 'Del Peak 8(4q28.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 8(4q28.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000189 (Fisher's exact test), Q value = 0.046

Table S11. Gene #29: 'Del Peak 8(4q28.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	77	55
DEL PEAK 8(4Q28.2) MUTATED	12	5	0
DEL PEAK 8(4Q28.2) WILD-TYPE	43	72	55

Figure S11. Get High-res Image Gene #29: 'Del Peak 8(4q28.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 9(5q11.2) mutation analysis' versus 'CN_CNMF'

P value = 2.63e-07 (Fisher's exact test), Q value = 7e-05

Table S12. Gene #30: 'Del Peak 9(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 9(5Q11.2) MUTATED	9	2	19	0
DEL PEAK 9(5Q11.2) WILD-TYPE	25	90	40	2

Figure S12. Get High-res Image Gene #30: 'Del Peak 9(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 9(5q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.23

Table S13. Gene #30: 'Del Peak 9(5q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	77	55
DEL PEAK 9(5Q11.2) MUTATED	16	12	2
DEL PEAK 9(5Q11.2) WILD-TYPE	39	65	53

Figure S13. Get High-res Image Gene #30: 'Del Peak 9(5q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 10(5q21.1) mutation analysis' versus 'CN_CNMF'

P value = 9.42e-12 (Fisher's exact test), Q value = 2.6e-09

Table S14. Gene #31: 'Del Peak 10(5q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 10(5Q21.1) MUTATED	14	0	19	0
DEL PEAK 10(5Q21.1) WILD-TYPE	20	92	40	2

Figure S14. Get High-res Image Gene #31: 'Del Peak 10(5q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 10(5q21.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.77e-06 (Fisher's exact test), Q value = 0.00072

Table S15. Gene #31: 'Del Peak 10(5q21.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	77	55
DEL PEAK 10(5Q21.1) MUTATED	22	8	3
DEL PEAK 10(5Q21.1) WILD-TYPE	33	69	52

Figure S15. Get High-res Image Gene #31: 'Del Peak 10(5q21.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 11(6q15) mutation analysis' versus 'CN_CNMF'

P value = 2.58e-18 (Fisher's exact test), Q value = 7.3e-16

Table S16. Gene #32: 'Del Peak 11(6q15) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 11(6Q15) MUTATED	27	4	27	1
DEL PEAK 11(6Q15) WILD-TYPE	7	88	32	1

Figure S16. Get High-res Image Gene #32: 'Del Peak 11(6q15) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 11(6q15) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.94e-12 (Fisher's exact test), Q value = 2.5e-09

Table S17. Gene #32: 'Del Peak 11(6q15) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	77	55
DEL PEAK 11(6Q15) MUTATED	35	22	2
DEL PEAK 11(6Q15) WILD-TYPE	20	55	53

Figure S17. Get High-res Image Gene #32: 'Del Peak 11(6q15) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 11(6q15) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.13e-06 (Fisher's exact test), Q value = 3e-04

Table S18. Gene #32: 'Del Peak 11(6q15) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	53	63
DEL PEAK 11(6Q15) MUTATED	32	5	18
DEL PEAK 11(6Q15) WILD-TYPE	27	48	45

Figure S18. Get High-res Image Gene #32: 'Del Peak 11(6q15) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 11(6q15) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.91e-05 (Fisher's exact test), Q value = 0.0099

Table S19. Gene #32: 'Del Peak 11(6q15) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	75	51
DEL PEAK 11(6Q15) MUTATED	26	23	6
DEL PEAK 11(6Q15) WILD-TYPE	23	52	45

Figure S19. Get High-res Image Gene #32: 'Del Peak 11(6q15) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(6q15) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000276 (Fisher's exact test), Q value = 0.067

Table S20. Gene #32: 'Del Peak 11(6q15) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	46	25	60
DEL PEAK 11(6Q15) MUTATED	23	5	6	21
DEL PEAK 11(6Q15) WILD-TYPE	22	41	19	39

Figure S20. Get High-res Image Gene #32: 'Del Peak 11(6q15) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Del Peak 13(8p21.3) mutation analysis' versus 'CN_CNMF'

P value = 1.68e-08 (Fisher's exact test), Q value = 4.5e-06

Table S21. Gene #34: 'Del Peak 13(8p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 13(8P21.3) MUTATED	17	38	52	1
DEL PEAK 13(8P21.3) WILD-TYPE	17	54	7	1

Figure S21. Get High-res Image Gene #34: 'Del Peak 13(8p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 13(8p21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.8e-06 (Fisher's exact test), Q value = 0.00073

Table S22. Gene #34: 'Del Peak 13(8p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	77	55
DEL PEAK 13(8P21.3) MUTATED	31	59	18
DEL PEAK 13(8P21.3) WILD-TYPE	24	18	37

Figure S22. Get High-res Image Gene #34: 'Del Peak 13(8p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 13(8p21.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.83e-05 (Fisher's exact test), Q value = 0.017

Table S23. Gene #34: 'Del Peak 13(8p21.3) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	53	63
DEL PEAK 13(8P21.3) MUTATED	30	24	51
DEL PEAK 13(8P21.3) WILD-TYPE	29	29	12

Figure S23. Get High-res Image Gene #34: 'Del Peak 13(8p21.3) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 13(8p21.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000164 (Fisher's exact test), Q value = 0.041

Table S24. Gene #34: 'Del Peak 13(8p21.3) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	75	51
DEL PEAK 13(8P21.3) MUTATED	25	58	22
DEL PEAK 13(8P21.3) WILD-TYPE	24	17	29

Figure S24. Get High-res Image Gene #34: 'Del Peak 13(8p21.3) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(8p11.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000234 (Fisher's exact test), Q value = 0.057

Table S25. Gene #35: 'Del Peak 14(8p11.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	77	55
DEL PEAK 14(8P11.21) MUTATED	17	35	7
DEL PEAK 14(8P11.21) WILD-TYPE	38	42	48

Figure S25. Get High-res Image Gene #35: 'Del Peak 14(8p11.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 14(8p11.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000913 (Fisher's exact test), Q value = 0.22

Table S26. Gene #35: 'Del Peak 14(8p11.21) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	53	63
DEL PEAK 14(8P11.21) MUTATED	17	10	32
DEL PEAK 14(8P11.21) WILD-TYPE	42	43	31

Figure S26. Get High-res Image Gene #35: 'Del Peak 14(8p11.21) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 15(9p22.3) mutation analysis' versus 'CN_CNMF'

P value = 0.000599 (Fisher's exact test), Q value = 0.14

Table S27. Gene #36: 'Del Peak 15(9p22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 15(9P22.3) MUTATED	0	3	12	0
DEL PEAK 15(9P22.3) WILD-TYPE	34	89	47	2

Figure S27. Get High-res Image Gene #36: 'Del Peak 15(9p22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 16(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 7.27e-07 (Fisher's exact test), Q value = 0.00019

Table S28. Gene #37: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 16(10Q23.31) MUTATED	4	24	36	1
DEL PEAK 16(10Q23.31) WILD-TYPE	30	68	23	1

Figure S28. Get High-res Image Gene #37: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 16(10q23.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.01e-06 (Fisher's exact test), Q value = 0.00078

Table S29. Gene #37: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	77	55
DEL PEAK 16(10Q23.31) MUTATED	12	43	10
DEL PEAK 16(10Q23.31) WILD-TYPE	43	34	45

Figure S29. Get High-res Image Gene #37: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 16(10q23.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.72e-08 (Fisher's exact test), Q value = 1.3e-05

Table S30. Gene #37: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	53	63
DEL PEAK 16(10Q23.31) MUTATED	13	9	40
DEL PEAK 16(10Q23.31) WILD-TYPE	46	44	23

Figure S30. Get High-res Image Gene #37: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 16(10q23.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-06 (Fisher's exact test), Q value = 0.00027

Table S31. Gene #37: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	75	51
DEL PEAK 16(10Q23.31) MUTATED	10	43	9
DEL PEAK 16(10Q23.31) WILD-TYPE	39	32	42

Figure S31. Get High-res Image Gene #37: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(12p13.2) mutation analysis' versus 'CN_CNMF'

P value = 7.1e-05 (Fisher's exact test), Q value = 0.018

Table S32. Gene #39: 'Del Peak 18(12p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 18(12P13.2) MUTATED	6	9	24	0
DEL PEAK 18(12P13.2) WILD-TYPE	28	83	35	2

Figure S32. Get High-res Image Gene #39: 'Del Peak 18(12p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 19(13q14.13) mutation analysis' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.077

Table S33. Gene #40: 'Del Peak 19(13q14.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 19(13Q14.13) MUTATED	21	27	34	1
DEL PEAK 19(13Q14.13) WILD-TYPE	13	65	25	1

Figure S33. Get High-res Image Gene #40: 'Del Peak 19(13q14.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 20(16q24.1) mutation analysis' versus 'CN_CNMF'

P value = 3.33e-10 (Fisher's exact test), Q value = 9.1e-08

Table S34. Gene #41: 'Del Peak 20(16q24.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 20(16Q24.1) MUTATED	7	23	44	0
DEL PEAK 20(16Q24.1) WILD-TYPE	27	69	15	2

Figure S34. Get High-res Image Gene #41: 'Del Peak 20(16q24.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 21(17p13.1) mutation analysis' versus 'CN_CNMF'

P value = 2.13e-09 (Fisher's exact test), Q value = 5.7e-07

Table S35. Gene #42: 'Del Peak 21(17p13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 21(17P13.1) MUTATED	3	10	32	1
DEL PEAK 21(17P13.1) WILD-TYPE	31	82	27	1

Figure S35. Get High-res Image Gene #42: 'Del Peak 21(17p13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 22(17q21.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.14e-05 (Fisher's exact test), Q value = 0.008

Table S36. Gene #43: 'Del Peak 22(17q21.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	77	55
DEL PEAK 22(17Q21.31) MUTATED	4	27	5
DEL PEAK 22(17Q21.31) WILD-TYPE	51	50	50

Figure S36. Get High-res Image Gene #43: 'Del Peak 22(17q21.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 22(17q21.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.6e-05 (Fisher's exact test), Q value = 0.0066

Table S37. Gene #43: 'Del Peak 22(17q21.31) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	53	63
DEL PEAK 22(17Q21.31) MUTATED	6	4	24
DEL PEAK 22(17Q21.31) WILD-TYPE	53	49	39

Figure S37. Get High-res Image Gene #43: 'Del Peak 22(17q21.31) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 22(17q21.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.54e-05 (Fisher's exact test), Q value = 0.014

Table S38. Gene #43: 'Del Peak 22(17q21.31) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	75	51
DEL PEAK 22(17Q21.31) MUTATED	3	26	5
DEL PEAK 22(17Q21.31) WILD-TYPE	46	49	46

Figure S38. Get High-res Image Gene #43: 'Del Peak 22(17q21.31) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 23(18q22.1) mutation analysis' versus 'CN_CNMF'

P value = 7.86e-10 (Fisher's exact test), Q value = 2.1e-07

Table S39. Gene #44: 'Del Peak 23(18q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 23(18Q22.1) MUTATED	3	10	33	0
DEL PEAK 23(18Q22.1) WILD-TYPE	31	82	26	2

Figure S39. Get High-res Image Gene #44: 'Del Peak 23(18q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 24(18q23) mutation analysis' versus 'CN_CNMF'

P value = 7.39e-14 (Fisher's exact test), Q value = 2.1e-11

Table S40. Gene #45: 'Del Peak 24(18q23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 24(18Q23) MUTATED	4	9	39	0
DEL PEAK 24(18Q23) WILD-TYPE	30	83	20	2

Figure S40. Get High-res Image Gene #45: 'Del Peak 24(18q23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 25(21q22.2) mutation analysis' versus 'CN_CNMF'

P value = 1.94e-06 (Fisher's exact test), Q value = 0.00051

Table S41. Gene #46: 'Del Peak 25(21q22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 25(21Q22.2) MUTATED	0	37	23	1
DEL PEAK 25(21Q22.2) WILD-TYPE	34	55	36	1

Figure S41. Get High-res Image Gene #46: 'Del Peak 25(21q22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 25(21q22.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.96e-14 (Fisher's exact test), Q value = 2.2e-11

Table S42. Gene #46: 'Del Peak 25(21q22.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	77	55
DEL PEAK 25(21Q22.2) MUTATED	4	49	8
DEL PEAK 25(21Q22.2) WILD-TYPE	51	28	47

Figure S42. Get High-res Image Gene #46: 'Del Peak 25(21q22.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 25(21q22.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.59e-10 (Fisher's exact test), Q value = 1.8e-07

Table S43. Gene #46: 'Del Peak 25(21q22.2) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	53	63
DEL PEAK 25(21Q22.2) MUTATED	5	14	39
DEL PEAK 25(21Q22.2) WILD-TYPE	54	39	24

Figure S43. Get High-res Image Gene #46: 'Del Peak 25(21q22.2) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 25(21q22.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.91e-12 (Fisher's exact test), Q value = 5.3e-10

Table S44. Gene #46: 'Del Peak 25(21q22.2) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	75	51
DEL PEAK 25(21Q22.2) MUTATED	2	46	10
DEL PEAK 25(21Q22.2) WILD-TYPE	47	29	41

Figure S44. Get High-res Image Gene #46: 'Del Peak 25(21q22.2) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 26(21q22.3) mutation analysis' versus 'CN_CNMF'

P value = 1.77e-06 (Fisher's exact test), Q value = 0.00046

Table S45. Gene #47: 'Del Peak 26(21q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 26(21Q22.3) MUTATED	0	38	22	0
DEL PEAK 26(21Q22.3) WILD-TYPE	34	54	37	2

Figure S45. Get High-res Image Gene #47: 'Del Peak 26(21q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 26(21q22.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.56e-13 (Fisher's exact test), Q value = 1.6e-10

Table S46. Gene #47: 'Del Peak 26(21q22.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	77	55
DEL PEAK 26(21Q22.3) MUTATED	5	48	7
DEL PEAK 26(21Q22.3) WILD-TYPE	50	29	48

Figure S46. Get High-res Image Gene #47: 'Del Peak 26(21q22.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 26(21q22.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 9.24e-11 (Fisher's exact test), Q value = 2.5e-08

Table S47. Gene #47: 'Del Peak 26(21q22.3) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	53	63
DEL PEAK 26(21Q22.3) MUTATED	5	12	40
DEL PEAK 26(21Q22.3) WILD-TYPE	54	41	23

Figure S47. Get High-res Image Gene #47: 'Del Peak 26(21q22.3) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 26(21q22.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.05e-13 (Fisher's exact test), Q value = 2.2e-10

Table S48. Gene #47: 'Del Peak 26(21q22.3) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	75	51
DEL PEAK 26(21Q22.3) MUTATED	2	46	9
DEL PEAK 26(21Q22.3) WILD-TYPE	47	29	42

Figure S48. Get High-res Image Gene #47: 'Del Peak 26(21q22.3) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 26(21q22.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.042

Table S49. Gene #47: 'Del Peak 26(21q22.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	69	77
DEL PEAK 26(21Q22.3) MUTATED	3	34	20
DEL PEAK 26(21Q22.3) WILD-TYPE	27	35	57

Figure S49. Get High-res Image Gene #47: 'Del Peak 26(21q22.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = PRAD-TP.transferedmergedcluster.txt
Number of patients = 187
Number of copy number variation regions = 47
Number of molecular subtypes = 6
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] 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)

[3] GISTIC_version2

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