Correlation between copy number variation genes and molecular subtypes

Prostate Adenocarcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_23

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 (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1445JKT

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 8 molecular subtypes across 187 patients, 47 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'.
Amp Peak 5(8p11.22) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(8q21.13) cnvs correlated to 'CN_CNMF' and 'METHLYATION_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' and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 8(4q28.2) cnvs correlated to 'CN_CNMF'.
Del Peak 9(5q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 10(5q21.1) cnvs correlated to 'CN_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', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 14(8p11.21) cnvs correlated to 'METHLYATION_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' and 'MIRSEQ_MATURE_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', and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 47 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 47 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE 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	Chi-square test	Fisher's exact test
Del Peak 11(6q15)	0 (0%)	128	2.58e-18 (9.72e-16)	2.16e-08 (7.83e-06)	1.13e-06 (0.000403)	3.91e-05 (0.0136)	4.64e-05 (0.0161)	0.0325 (1.00)	0.00441 (1.00)	0.284 (1.00)
Del Peak 13(8p21 3)	0 (0%)	79	1.68e-08 (6.1e-06)	2.28e-06 (0.000805)	6.83e-05 (0.0234)	0.000164 (0.0557)	0.0133 (1.00)	0.304 (1.00)	2.55e-05 (0.00891)	0.0741 (1.00)
Del Peak 16(10q23 31)	0 (0%)	122	7.27e-07 (0.00026)	2.12e-07 (7.62e-05)	4.72e-08 (1.71e-05)	1e-06 (0.000359)	0.0189 (1.00)	0.115 (1.00)	0.00192 (0.61)	0.423 (1.00)
Del Peak 25(21q22 2)	0 (0%)	126	1.94e-06 (0.000688)	1.3e-12 (4.85e-10)	6.59e-10 (2.41e-07)	1.91e-12 (7.11e-10)	0.0797 (1.00)	0.017 (1.00)	0.27 (1.00)	0.118 (1.00)
Del Peak 26(21q22 3)	0 (0%)	127	1.77e-06 (0.000627)	2.54e-12 (9.41e-10)	9.24e-11 (3.41e-08)	8.05e-13 (3.01e-10)	0.0301 (1.00)	0.00157 (0.502)	0.00442 (1.00)	0.0251 (1.00)
Del Peak 22(17q21 31)	0 (0%)	151	0.00697 (1.00)	0.000116 (0.0397)	2.6e-05 (0.00907)	5.54e-05 (0.0191)	0.0594 (1.00)	0.211 (1.00)	0.103 (1.00)	0.495 (1.00)
Amp Peak 6(8q21 13)	0 (0%)	141	4.82e-10 (1.77e-07)	0.000648 (0.214)	0.00137 (0.444)	0.00784 (1.00)	0.0717 (1.00)	0.0448 (1.00)	0.0857 (1.00)	0.737 (1.00)
Del Peak 5(2q22 1)	0 (0%)	165	6.01e-05 (0.0207)	0.0296 (1.00)	0.11 (1.00)	0.033 (1.00)	0.0262 (1.00)	0.000266 (0.0897)	0.0034 (1.00)	0.0153 (1.00)
Del Peak 18(12p13 2)	0 (0%)	148	7.1e-05 (0.0243)	0.0161 (1.00)	0.562 (1.00)	0.0963 (1.00)	0.307 (1.00)	0.361 (1.00)	0.000629 (0.208)	0.881 (1.00)
Amp Peak 2(3q26 2)	0 (0%)	160	0.0003 (0.101)	0.453 (1.00)	0.305 (1.00)	0.495 (1.00)	0.462 (1.00)	0.22 (1.00)	0.21 (1.00)	0.24 (1.00)
Amp Peak 3(7p15 3)	0 (0%)	152	3.5e-06 (0.00123)	0.0447 (1.00)	0.00785 (1.00)	0.0135 (1.00)	0.394 (1.00)	0.876 (1.00)	0.255 (1.00)	0.22 (1.00)
Amp Peak 4(7q34)	0 (0%)	155	0.000158 (0.0539)	0.0141 (1.00)	0.00179 (0.57)	0.000969 (0.316)	0.237 (1.00)	0.752 (1.00)	0.353 (1.00)	0.247 (1.00)
Amp Peak 5(8p11 22)	0 (0%)	170	1.44e-05 (0.00504)	0.149 (1.00)	0.0508 (1.00)	0.268 (1.00)	0.258 (1.00)	0.386 (1.00)	0.128 (1.00)	0.86 (1.00)
Amp Peak 7(11q13 2)	0 (0%)	176	0.000495 (0.165)	0.445 (1.00)	0.193 (1.00)	0.355 (1.00)	0.842 (1.00)	0.62 (1.00)	0.675 (1.00)	0.802 (1.00)
Del Peak 1(1p31 3)	0 (0%)	165	0.0439 (1.00)	0.000408 (0.136)	0.00169 (0.542)	0.00458 (1.00)	0.0262 (1.00)	0.513 (1.00)	0.226 (1.00)	0.291 (1.00)
Del Peak 8(4q28 2)	0 (0%)	170	0.000215 (0.0728)	0.0131 (1.00)	0.0149 (1.00)	0.0943 (1.00)	0.158 (1.00)	0.144 (1.00)	0.205 (1.00)	0.163 (1.00)
Del Peak 9(5q11 2)	0 (0%)	157	2.63e-07 (9.45e-05)	0.00146 (0.471)	0.0901 (1.00)	0.0433 (1.00)	0.0793 (1.00)	0.59 (1.00)	0.0108 (1.00)	0.773 (1.00)
Del Peak 10(5q21 1)	0 (0%)	154	9.42e-12 (3.49e-09)	0.00104 (0.337)	0.00269 (0.848)	0.00737 (1.00)	0.182 (1.00)	0.42 (1.00)	0.0083 (1.00)	0.618 (1.00)
Del Peak 14(8p11 21)	0 (0%)	128	0.0124 (1.00)	3.15e-05 (0.011)	0.000913 (0.3)	0.0164 (1.00)	0.361 (1.00)	0.933 (1.00)	0.0159 (1.00)	0.511 (1.00)
Del Peak 15(9p22 3)	0 (0%)	172	0.000599 (0.199)	0.497 (1.00)	0.216 (1.00)	0.268 (1.00)	0.615 (1.00)	1 (1.00)	0.759 (1.00)	1 (1.00)
Del Peak 19(13q14 13)	0 (0%)	104	0.00032 (0.107)	0.00449 (1.00)	0.00147 (0.473)	0.00478 (1.00)	0.412 (1.00)	0.534 (1.00)	0.0399 (1.00)	0.631 (1.00)
Del Peak 20(16q24 1)	0 (0%)	113	3.33e-10 (1.22e-07)	0.0009 (0.296)	0.0228 (1.00)	0.0158 (1.00)	0.0023 (0.728)	0.0277 (1.00)	0.0123 (1.00)	0.355 (1.00)
Del Peak 21(17p13 1)	0 (0%)	141	2.13e-09 (7.75e-07)	0.054 (1.00)	0.0284 (1.00)	0.00411 (1.00)	0.328 (1.00)	0.242 (1.00)	0.0087 (1.00)	0.737 (1.00)
Del Peak 23(18q22 1)	0 (0%)	141	7.86e-10 (2.87e-07)	0.0983 (1.00)	0.196 (1.00)	0.449 (1.00)	0.136 (1.00)	0.215 (1.00)	0.337 (1.00)	0.298 (1.00)
Del Peak 24(18q23)	0 (0%)	135	7.39e-14 (2.77e-11)	0.0623 (1.00)	0.0654 (1.00)	0.136 (1.00)	0.231 (1.00)	0.799 (1.00)	0.336 (1.00)	0.675 (1.00)
Amp Peak 1(1q21 3)	0 (0%)	175	0.0143 (1.00)	0.311 (1.00)	0.144 (1.00)	0.124 (1.00)	0.23 (1.00)	0.521 (1.00)	0.0243 (1.00)	1 (1.00)
Amp Peak 8(12q24 32)	0 (0%)	180	0.00207 (0.657)	0.474 (1.00)	0.894 (1.00)	0.183 (1.00)	0.895 (1.00)	0.857 (1.00)	0.297 (1.00)	0.211 (1.00)
Amp Peak 9(14q21 1)	0 (0%)	177	0.0333 (1.00)	0.00532 (1.00)	0.00905 (1.00)	0.518 (1.00)	0.241 (1.00)	0.203 (1.00)	0.47 (1.00)	0.109 (1.00)
Amp Peak 10(20q13 33)	0 (0%)	175	0.00575 (1.00)	0.000936 (0.306)	0.0118 (1.00)	0.00956 (1.00)	0.672 (1.00)	0.0711 (1.00)	0.0931 (1.00)	1 (1.00)
Amp Peak 11(21q21 3)	0 (0%)	180	0.0323 (1.00)	0.215 (1.00)	0.218 (1.00)	0.288 (1.00)	0.455 (1.00)	0.534 (1.00)	0.802 (1.00)	0.53 (1.00)
Amp Peak 12(Xp22 11)	0 (0%)	182	0.363 (1.00)	0.671 (1.00)	0.74 (1.00)	0.606 (1.00)	0.654 (1.00)	0.0892 (1.00)	0.158 (1.00)	0.122 (1.00)
Amp Peak 13(Xp22 11)	0 (0%)	182	0.726 (1.00)	0.351 (1.00)	1 (1.00)	0.735 (1.00)	0.545 (1.00)	0.393 (1.00)	0.293 (1.00)	0.7 (1.00)
Amp Peak 14(Xp21 1)	0 (0%)	183	0.68 (1.00)	0.0794 (1.00)	1 (1.00)	1 (1.00)	0.39 (1.00)	0.507 (1.00)	0.817 (1.00)	0.396 (1.00)
Amp Peak 15(Xq12)	0 (0%)	183	0.278 (1.00)	0.486 (1.00)	0.0637 (1.00)	0.021 (1.00)	0.593 (1.00)	0.387 (1.00)	0.657 (1.00)	0.656 (1.00)
Amp Peak 16(Xq21 1)	0 (0%)	180	0.39 (1.00)	0.215 (1.00)	0.199 (1.00)	0.234 (1.00)	0.776 (1.00)	0.408 (1.00)	0.663 (1.00)	0.361 (1.00)
Amp Peak 17(Xq21 1)	0 (0%)	182	0.363 (1.00)	0.122 (1.00)	0.529 (1.00)	0.332 (1.00)	0.82 (1.00)	0.716 (1.00)	0.568 (1.00)	1 (1.00)
Amp Peak 18(Xq21 31)	0 (0%)	182	0.139 (1.00)	0.476 (1.00)	0.325 (1.00)	0.138 (1.00)	0.937 (1.00)	0.853 (1.00)	0.607 (1.00)	0.7 (1.00)
Amp Peak 19(Xq25)	0 (0%)	183	0.0497 (1.00)	0.583 (1.00)	0.391 (1.00)	0.173 (1.00)	0.317 (1.00)	0.172 (1.00)	0.0606 (1.00)	0.198 (1.00)
Amp Peak 20(Xq25)	0 (0%)	181	1 (1.00)	0.0725 (1.00)	0.118 (1.00)	0.5 (1.00)	0.54 (1.00)	0.269 (1.00)	0.468 (1.00)	0.492 (1.00)
Amp Peak 21(Xq27 1)	0 (0%)	178	0.00666 (1.00)	0.624 (1.00)	0.835 (1.00)	0.831 (1.00)	0.0296 (1.00)	0.0345 (1.00)	0.0121 (1.00)	0.00988 (1.00)
Del Peak 2(1p21 3)	0 (0%)	171	0.00945 (1.00)	0.648 (1.00)	0.945 (1.00)	1 (1.00)	0.446 (1.00)	0.609 (1.00)	0.194 (1.00)	0.163 (1.00)
Del Peak 3(1q23 1)	0 (0%)	179	0.096 (1.00)	0.138 (1.00)	0.136 (1.00)	0.111 (1.00)	0.0916 (1.00)	0.0422 (1.00)	0.279 (1.00)	0.136 (1.00)
Del Peak 4(1q42 13)	0 (0%)	169	0.448 (1.00)	0.0973 (1.00)	0.73 (1.00)	0.807 (1.00)	0.85 (1.00)	0.534 (1.00)	0.481 (1.00)	1 (1.00)
Del Peak 6(3p13)	0 (0%)	159	0.668 (1.00)	0.0336 (1.00)	0.294 (1.00)	0.0302 (1.00)	0.193 (1.00)	0.856 (1.00)	0.433 (1.00)	0.106 (1.00)
Del Peak 7(3q29)	0 (0%)	175	0.768 (1.00)	0.0689 (1.00)	0.0694 (1.00)	0.0229 (1.00)	0.851 (1.00)	0.855 (1.00)	0.618 (1.00)	0.53 (1.00)
Del Peak 12(7q36 1)	0 (0%)	178	0.382 (1.00)	0.139 (1.00)	0.596 (1.00)	0.483 (1.00)	0.289 (1.00)	0.481 (1.00)	0.523 (1.00)	0.784 (1.00)
Del Peak 17(11q23 2)	0 (0%)	164	0.0629 (1.00)	0.482 (1.00)	0.877 (1.00)	0.916 (1.00)	0.0966 (1.00)	0.346 (1.00)	0.258 (1.00)	0.897 (1.00)

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

P value = 3e-04 (Fisher's exact test), Q value = 0.1

Table S1. Gene #2: 'Amp Peak 2(3q26.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
AMP PEAK 2(3Q26.2) CNV	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)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 3.5e-06 (Fisher's exact test), Q value = 0.0012

Table S2. Gene #3: 'Amp Peak 3(7p15.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
AMP PEAK 3(7P15.3) CNV	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)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000158 (Fisher's exact test), Q value = 0.054

Table S3. Gene #4: 'Amp Peak 4(7q34)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
AMP PEAK 4(7Q34) CNV	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)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 1.44e-05 (Fisher's exact test), Q value = 0.005

Table S4. Gene #5: 'Amp Peak 5(8p11.22)' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S4. Get High-res Image Gene #5: 'Amp Peak 5(8p11.22)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 4.82e-10 (Fisher's exact test), Q value = 1.8e-07

Table S5. Gene #6: 'Amp Peak 6(8q21.13)' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S5. Get High-res Image Gene #6: 'Amp Peak 6(8q21.13)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 6(8q21.13)' versus 'METHLYATION_CNMF'

P value = 0.000648 (Fisher's exact test), Q value = 0.21

Table S6. Gene #6: 'Amp Peak 6(8q21.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	57	55	18
AMP PEAK 6(8Q21.13) CNV	24	13	5	4
AMP PEAK 6(8Q21.13) WILD-TYPE	33	44	50	14

Figure S6. Get High-res Image Gene #6: 'Amp Peak 6(8q21.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 0.000495 (Fisher's exact test), Q value = 0.16

Table S7. Gene #7: 'Amp Peak 7(11q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
AMP PEAK 7(11Q13.2) CNV	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)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000408 (Fisher's exact test), Q value = 0.14

Table S8. Gene #22: 'Del Peak 1(1p31.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	57	55	18
DEL PEAK 1(1P31.3) CNV	4	15	1	2
DEL PEAK 1(1P31.3) WILD-TYPE	53	42	54	16

Figure S8. Get High-res Image Gene #22: 'Del Peak 1(1p31.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 6.01e-05 (Fisher's exact test), Q value = 0.021

Table S9. Gene #26: 'Del Peak 5(2q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 5(2Q22.1) CNV	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)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 5(2q22.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000266 (Fisher's exact test), Q value = 0.09

Table S10. Gene #26: 'Del Peak 5(2q22.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	64	90
DEL PEAK 5(2Q22.1) CNV	2	1	19
DEL PEAK 5(2Q22.1) WILD-TYPE	30	63	71

Figure S10. Get High-res Image Gene #26: 'Del Peak 5(2q22.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000215 (Fisher's exact test), Q value = 0.073

Table S11. Gene #29: 'Del Peak 8(4q28.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S11. Get High-res Image Gene #29: 'Del Peak 8(4q28.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.63e-07 (Fisher's exact test), Q value = 9.4e-05

Table S12. Gene #30: 'Del Peak 9(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	92	59	2
DEL PEAK 9(5Q11.2) CNV	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)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 9.42e-12 (Fisher's exact test), Q value = 3.5e-09

Table S13. Gene #31: 'Del Peak 10(5q21.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S13. Get High-res Image Gene #31: 'Del Peak 10(5q21.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.58e-18 (Fisher's exact test), Q value = 9.7e-16

Table S14. Gene #32: 'Del Peak 11(6q15)' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S14. Get High-res Image Gene #32: 'Del Peak 11(6q15)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.16e-08 (Fisher's exact test), Q value = 7.8e-06

Table S15. Gene #32: 'Del Peak 11(6q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	57	55	18
DEL PEAK 11(6Q15) CNV	34	16	4	5
DEL PEAK 11(6Q15) WILD-TYPE	23	41	51	13

Figure S15. Get High-res Image Gene #32: 'Del Peak 11(6q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 1.13e-06 (Fisher's exact test), Q value = 4e-04

Table S16. Gene #32: 'Del Peak 11(6q15)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

Figure S16. Get High-res Image Gene #32: 'Del Peak 11(6q15)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 3.91e-05 (Fisher's exact test), Q value = 0.014

Table S17. Gene #32: 'Del Peak 11(6q15)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

Figure S17. Get High-res Image Gene #32: 'Del Peak 11(6q15)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

P value = 4.64e-05 (Fisher's exact test), Q value = 0.016

Table S18. Gene #32: 'Del Peak 11(6q15)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	51	28	55
DEL PEAK 11(6Q15) CNV	27	5	8	18
DEL PEAK 11(6Q15) WILD-TYPE	25	46	20	37

Figure S18. Get High-res Image Gene #32: 'Del Peak 11(6q15)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 1.68e-08 (Fisher's exact test), Q value = 6.1e-06

Table S19. Gene #34: 'Del Peak 13(8p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S19. Get High-res Image Gene #34: 'Del Peak 13(8p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.28e-06 (Fisher's exact test), Q value = 8e-04

Table S20. Gene #34: 'Del Peak 13(8p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	57	55	18
DEL PEAK 13(8P21.3) CNV	33	43	17	15
DEL PEAK 13(8P21.3) WILD-TYPE	24	14	38	3

Figure S20. Get High-res Image Gene #34: 'Del Peak 13(8p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 6.83e-05 (Fisher's exact test), Q value = 0.023

Table S21. Gene #34: 'Del Peak 13(8p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

Figure S21. Get High-res Image Gene #34: 'Del Peak 13(8p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 0.000164 (Fisher's exact test), Q value = 0.056

Table S22. Gene #34: 'Del Peak 13(8p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

Figure S22. Get High-res Image Gene #34: 'Del Peak 13(8p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(8p21.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.55e-05 (Chi-square test), Q value = 0.0089

Table S23. Gene #34: 'Del Peak 13(8p21.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	30	32	22	58
DEL PEAK 13(8P21.3) CNV	33	7	22	8	37
DEL PEAK 13(8P21.3) WILD-TYPE	11	23	10	14	21

Figure S23. Get High-res Image Gene #34: 'Del Peak 13(8p21.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

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

P value = 3.15e-05 (Fisher's exact test), Q value = 0.011

Table S24. Gene #35: 'Del Peak 14(8p11.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	57	55	18
DEL PEAK 14(8P11.21) CNV	19	26	5	9
DEL PEAK 14(8P11.21) WILD-TYPE	38	31	50	9

Figure S24. Get High-res Image Gene #35: 'Del Peak 14(8p11.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 0.000599 (Fisher's exact test), Q value = 0.2

Table S25. Gene #36: 'Del Peak 15(9p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S25. Get High-res Image Gene #36: 'Del Peak 15(9p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 7.27e-07 (Fisher's exact test), Q value = 0.00026

Table S26. Gene #37: 'Del Peak 16(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S26. Get High-res Image Gene #37: 'Del Peak 16(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.12e-07 (Fisher's exact test), Q value = 7.6e-05

Table S27. Gene #37: 'Del Peak 16(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	57	55	18
DEL PEAK 16(10Q23.31) CNV	13	35	8	9
DEL PEAK 16(10Q23.31) WILD-TYPE	44	22	47	9

Figure S27. Get High-res Image Gene #37: 'Del Peak 16(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 4.72e-08 (Fisher's exact test), Q value = 1.7e-05

Table S28. Gene #37: 'Del Peak 16(10q23.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

Figure S28. Get High-res Image Gene #37: 'Del Peak 16(10q23.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 1e-06 (Fisher's exact test), Q value = 0.00036

Table S29. Gene #37: 'Del Peak 16(10q23.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

Figure S29. Get High-res Image Gene #37: 'Del Peak 16(10q23.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

P value = 7.1e-05 (Fisher's exact test), Q value = 0.024

Table S30. Gene #39: 'Del Peak 18(12p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S30. Get High-res Image Gene #39: 'Del Peak 18(12p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 18(12p13.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000629 (Chi-square test), Q value = 0.21

Table S31. Gene #39: 'Del Peak 18(12p13.2)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	30	32	22	58
DEL PEAK 18(12P13.2) CNV	15	1	12	2	8
DEL PEAK 18(12P13.2) WILD-TYPE	29	29	20	20	50

Figure S31. Get High-res Image Gene #39: 'Del Peak 18(12p13.2)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

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

P value = 0.00032 (Fisher's exact test), Q value = 0.11

Table S32. Gene #40: 'Del Peak 19(13q14.13)' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S32. Get High-res Image Gene #40: 'Del Peak 19(13q14.13)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 3.33e-10 (Fisher's exact test), Q value = 1.2e-07

Table S33. Gene #41: 'Del Peak 20(16q24.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S33. Get High-res Image Gene #41: 'Del Peak 20(16q24.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.13e-09 (Fisher's exact test), Q value = 7.8e-07

Table S34. Gene #42: 'Del Peak 21(17p13.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S34. Get High-res Image Gene #42: 'Del Peak 21(17p13.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000116 (Fisher's exact test), Q value = 0.04

Table S35. Gene #43: 'Del Peak 22(17q21.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	57	55	18
DEL PEAK 22(17Q21.31) CNV	5	22	5	4
DEL PEAK 22(17Q21.31) WILD-TYPE	52	35	50	14

Figure S35. Get High-res Image Gene #43: 'Del Peak 22(17q21.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 2.6e-05 (Fisher's exact test), Q value = 0.0091

Table S36. Gene #43: 'Del Peak 22(17q21.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

Figure S36. Get High-res Image Gene #43: 'Del Peak 22(17q21.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 5.54e-05 (Fisher's exact test), Q value = 0.019

Table S37. Gene #43: 'Del Peak 22(17q21.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

Figure S37. Get High-res Image Gene #43: 'Del Peak 22(17q21.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

P value = 7.86e-10 (Fisher's exact test), Q value = 2.9e-07

Table S38. Gene #44: 'Del Peak 23(18q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S38. Get High-res Image Gene #44: 'Del Peak 23(18q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 7.39e-14 (Fisher's exact test), Q value = 2.8e-11

Table S39. Gene #45: 'Del Peak 24(18q23)' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S39. Get High-res Image Gene #45: 'Del Peak 24(18q23)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 1.94e-06 (Fisher's exact test), Q value = 0.00069

Table S40. Gene #46: 'Del Peak 25(21q22.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S40. Get High-res Image Gene #46: 'Del Peak 25(21q22.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 1.3e-12 (Fisher's exact test), Q value = 4.8e-10

Table S41. Gene #46: 'Del Peak 25(21q22.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	57	55	18
DEL PEAK 25(21Q22.2) CNV	4	33	10	14
DEL PEAK 25(21Q22.2) WILD-TYPE	53	24	45	4

Figure S41. Get High-res Image Gene #46: 'Del Peak 25(21q22.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 6.59e-10 (Fisher's exact test), Q value = 2.4e-07

Table S42. Gene #46: 'Del Peak 25(21q22.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

Figure S42. Get High-res Image Gene #46: 'Del Peak 25(21q22.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 1.91e-12 (Fisher's exact test), Q value = 7.1e-10

Table S43. Gene #46: 'Del Peak 25(21q22.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

Figure S43. Get High-res Image Gene #46: 'Del Peak 25(21q22.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.77e-06 (Fisher's exact test), Q value = 0.00063

Table S44. Gene #47: 'Del Peak 26(21q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S44. Get High-res Image Gene #47: 'Del Peak 26(21q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.54e-12 (Fisher's exact test), Q value = 9.4e-10

Table S45. Gene #47: 'Del Peak 26(21q22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	57	55	18
DEL PEAK 26(21Q22.3) CNV	5	31	9	15
DEL PEAK 26(21Q22.3) WILD-TYPE	52	26	46	3

Figure S45. Get High-res Image Gene #47: 'Del Peak 26(21q22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 9.24e-11 (Fisher's exact test), Q value = 3.4e-08

Table S46. Gene #47: 'Del Peak 26(21q22.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

Figure S46. Get High-res Image Gene #47: 'Del Peak 26(21q22.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 8.05e-13 (Fisher's exact test), Q value = 3e-10

Table S47. Gene #47: 'Del Peak 26(21q22.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

Figure S47. Get High-res Image Gene #47: 'Del Peak 26(21q22.3)' versus Molecular Subtype #4: 'MRNASEQ_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 = 8
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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

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

Download Results

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

References

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

[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

[4] GISTIC_version2

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