Correlation between copy number variation genes and molecular subtypes

Pancreatic 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/C14B2ZC1

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 35 peak regions and 8 molecular subtypes across 50 patients, 42 significant findings detected with Q value < 0.25.

Amp Peak 3(7q22.1) cnvs correlated to 'METHLYATION_CNMF'.
Amp Peak 4(8q24.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(12p13.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(12p12.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 8(18q11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 9(20q13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 2(1p21.2) cnvs correlated to 'CN_CNMF'.
Del Peak 5(6p25.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 6(6p22.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 7(6q22.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 9(8p23.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 11(9p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 13(10q23.2) cnvs correlated to 'CN_CNMF'.
Del Peak 16(12q12) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 17(12q24.32) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 18(15q15.1) cnvs correlated to 'CN_CNMF'.
Del Peak 19(17p11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 20(17q23.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 21(18q21.2) cnvs correlated to 'CN_CNMF'.
Del Peak 24(Xq21.1) cnvs correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 35 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 42 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	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 7(6q22 33)	0 (0%)	24	3.74e-05 (0.00998)	2.99e-06 (0.000827)	0.000168 (0.0429)	2.98e-05 (0.00804)	0.000423 (0.104)	0.000497 (0.122)	0.000203 (0.0512)	2.16e-05 (0.00586)
Del Peak 11(9p21 3)	0 (0%)	20	2.64e-07 (7.37e-05)	4.84e-06 (0.00133)	0.0253 (1.00)	9.17e-06 (0.0025)	0.00971 (1.00)	0.00301 (0.702)	0.000203 (0.0512)	0.000234 (0.0585)
Del Peak 9(8p23 1)	0 (0%)	35	5e-05 (0.0132)	0.000859 (0.205)	0.0158 (1.00)	0.000786 (0.189)	0.00467 (1.00)	0.0035 (0.808)	0.000196 (0.0496)	0.0035 (0.808)
Del Peak 17(12q24 32)	0 (0%)	34	0.000769 (0.186)	0.0128 (1.00)	0.00392 (0.895)	0.000759 (0.184)	0.0589 (1.00)	0.0138 (1.00)	6.13e-05 (0.0162)	0.0138 (1.00)
Del Peak 19(17p11 2)	0 (0%)	31	0.000191 (0.0485)	2.77e-06 (0.00077)	0.0219 (1.00)	6.2e-05 (0.0163)	0.0687 (1.00)	0.066 (1.00)	0.00405 (0.915)	0.0197 (1.00)
Del Peak 20(17q23 2)	0 (0%)	35	0.000106 (0.0277)	0.000151 (0.039)	0.0341 (1.00)	0.00297 (0.696)	0.0215 (1.00)	0.00955 (1.00)	0.000567 (0.139)	0.00955 (1.00)
Del Peak 5(6p25 2)	0 (0%)	29	0.000139 (0.036)	4.59e-05 (0.0122)	0.027 (1.00)	0.00126 (0.297)	0.0454 (1.00)	0.223 (1.00)	0.0618 (1.00)	0.0597 (1.00)
Del Peak 6(6p22 3)	0 (0%)	30	0.0003 (0.0746)	0.000136 (0.0353)	0.00982 (1.00)	0.00395 (0.897)	0.0648 (1.00)	0.11 (1.00)	0.0268 (1.00)	0.0329 (1.00)
Amp Peak 3(7q22 1)	0 (0%)	36	0.0457 (1.00)	0.00085 (0.204)	0.133 (1.00)	0.0851 (1.00)	0.0441 (1.00)	0.257 (1.00)	0.0339 (1.00)	0.257 (1.00)
Amp Peak 4(8q24 21)	0 (0%)	29	0.000694 (0.169)	0.0484 (1.00)	0.216 (1.00)	0.00381 (0.872)	0.501 (1.00)	0.301 (1.00)	0.0666 (1.00)	0.144 (1.00)
Amp Peak 6(12p13 33)	0 (0%)	41	2.79e-06 (0.000772)	0.0129 (1.00)	0.186 (1.00)	0.0341 (1.00)	0.227 (1.00)	0.0847 (1.00)	0.0459 (1.00)	0.0847 (1.00)
Amp Peak 7(12p12 1)	0 (0%)	41	0.000327 (0.0812)	0.0129 (1.00)	0.0212 (1.00)	0.0341 (1.00)	0.0877 (1.00)	0.0562 (1.00)	0.0089 (1.00)	0.0562 (1.00)
Amp Peak 8(18q11 2)	0 (0%)	36	3.62e-05 (0.00969)	0.0231 (1.00)	0.0888 (1.00)	0.0136 (1.00)	0.063 (1.00)	0.0138 (1.00)	0.0883 (1.00)	0.0138 (1.00)
Amp Peak 9(20q13 2)	0 (0%)	36	0.000157 (0.0404)	0.394 (1.00)	0.721 (1.00)	0.231 (1.00)	0.792 (1.00)	0.467 (1.00)	0.31 (1.00)	0.467 (1.00)
Del Peak 2(1p21 2)	0 (0%)	39	5.64e-06 (0.00154)	0.0372 (1.00)	0.412 (1.00)	0.104 (1.00)	0.135 (1.00)	0.0367 (1.00)	0.0212 (1.00)	0.114 (1.00)
Del Peak 13(10q23 2)	0 (0%)	38	0.000159 (0.0408)	0.111 (1.00)	0.241 (1.00)	0.0535 (1.00)	0.255 (1.00)	0.0155 (1.00)	0.0689 (1.00)	0.0155 (1.00)
Del Peak 16(12q12)	0 (0%)	41	0.00456 (1.00)	3.27e-05 (0.00879)	0.0948 (1.00)	0.0101 (1.00)	0.172 (1.00)	0.0562 (1.00)	0.0946 (1.00)	0.0562 (1.00)
Del Peak 18(15q15 1)	0 (0%)	40	7.9e-05 (0.0207)	0.0895 (1.00)	0.412 (1.00)	0.104 (1.00)	0.331 (1.00)	0.114 (1.00)	0.132 (1.00)	0.114 (1.00)
Del Peak 21(18q21 2)	0 (0%)	18	0.000918 (0.219)	0.00334 (0.774)	0.196 (1.00)	0.00705 (1.00)	0.114 (1.00)	0.0725 (1.00)	0.0305 (1.00)	0.0264 (1.00)
Del Peak 24(Xq21 1)	0 (0%)	43	9.13e-06 (0.00249)	0.018 (1.00)	1 (1.00)	0.482 (1.00)	0.174 (1.00)	0.396 (1.00)	0.185 (1.00)	0.396 (1.00)
Amp Peak 1(1p34 3)	0 (0%)	44	0.0504 (1.00)	0.358 (1.00)	1 (1.00)	0.746 (1.00)	0.983 (1.00)	0.828 (1.00)	1 (1.00)	0.828 (1.00)
Amp Peak 2(1p12)	0 (0%)	41	0.0184 (1.00)	0.104 (1.00)	0.664 (1.00)	0.828 (1.00)	0.0479 (1.00)	0.621 (1.00)	1 (1.00)	0.621 (1.00)
Amp Peak 5(9p13 3)	0 (0%)	44	0.011 (1.00)	0.547 (1.00)	0.345 (1.00)	0.482 (1.00)	0.198 (1.00)	0.249 (1.00)	0.345 (1.00)	0.249 (1.00)
Amp Peak 10(Xp22 11)	0 (0%)	47	0.769 (1.00)	0.777 (1.00)	1 (1.00)		0.783 (1.00)	0.592 (1.00)	0.607 (1.00)	0.592 (1.00)
Amp Peak 11(Xq27 1)	0 (0%)	44	0.0365 (1.00)	0.749 (1.00)	0.172 (1.00)	0.8 (1.00)	0.634 (1.00)	0.729 (1.00)	1 (1.00)	0.729 (1.00)
Del Peak 1(1p36 22)	0 (0%)	37	0.00124 (0.293)	0.00414 (0.932)	0.0948 (1.00)	0.104 (1.00)	0.0732 (1.00)	0.0367 (1.00)	0.132 (1.00)	0.114 (1.00)
Del Peak 3(4p12)	0 (0%)	45	0.0105 (1.00)	0.13 (1.00)	0.108 (1.00)	0.184 (1.00)	0.353 (1.00)	0.0637 (1.00)	0.108 (1.00)	0.0637 (1.00)
Del Peak 4(5q14 2)	0 (0%)	41	0.00717 (1.00)	0.898 (1.00)	1 (1.00)	0.828 (1.00)	0.979 (1.00)	0.887 (1.00)	0.24 (1.00)	0.887 (1.00)
Del Peak 8(7q36 1)	0 (0%)	45	0.0217 (1.00)	0.0575 (1.00)	0.108 (1.00)	0.184 (1.00)	0.108 (1.00)	0.515 (1.00)	0.108 (1.00)	0.515 (1.00)
Del Peak 10(8q12 1)	0 (0%)	47	0.143 (1.00)	0.341 (1.00)	1 (1.00)	1 (1.00)	0.783 (1.00)	0.417 (1.00)	1 (1.00)	0.417 (1.00)
Del Peak 12(9p13 2)	0 (0%)	31	0.0136 (1.00)	0.117 (1.00)	0.511 (1.00)	0.116 (1.00)	0.32 (1.00)	0.409 (1.00)	0.104 (1.00)	0.409 (1.00)
Del Peak 14(11p15 4)	0 (0%)	40	0.00661 (1.00)	0.402 (1.00)	0.698 (1.00)	0.254 (1.00)	0.556 (1.00)	0.528 (1.00)	0.24 (1.00)	0.528 (1.00)
Del Peak 15(12p12 3)	0 (0%)	42	0.0109 (1.00)	0.00254 (0.597)	0.0486 (1.00)	0.0605 (1.00)	0.0876 (1.00)	0.00756 (1.00)	0.0211 (1.00)	0.00756 (1.00)
Del Peak 22(21q22 11)	0 (0%)	31	0.0226 (1.00)	0.334 (1.00)	0.0455 (1.00)	0.0301 (1.00)	0.187 (1.00)	0.029 (1.00)	0.0217 (1.00)	0.0986 (1.00)
Del Peak 23(22q13 31)	0 (0%)	36	0.00708 (1.00)	0.0656 (1.00)	0.281 (1.00)	0.067 (1.00)	0.167 (1.00)	0.0317 (1.00)	0.162 (1.00)	0.0317 (1.00)

'Amp Peak 3(7q22.1)' versus 'METHLYATION_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.2

Table S1. Gene #3: 'Amp Peak 3(7q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	19	12
AMP PEAK 3(7Q22.1) CNV	7	0	6
AMP PEAK 3(7Q22.1) WILD-TYPE	11	19	6

Figure S1. Get High-res Image Gene #3: 'Amp Peak 3(7q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 4(8q24.21)' versus 'CN_CNMF'

P value = 0.000694 (Fisher's exact test), Q value = 0.17

Table S2. Gene #4: 'Amp Peak 4(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
AMP PEAK 4(8Q24.21) CNV	10	6	5
AMP PEAK 4(8Q24.21) WILD-TYPE	2	22	5

Figure S2. Get High-res Image Gene #4: 'Amp Peak 4(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 6(12p13.33)' versus 'CN_CNMF'

P value = 2.79e-06 (Fisher's exact test), Q value = 0.00077

Table S3. Gene #6: 'Amp Peak 6(12p13.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
AMP PEAK 6(12P13.33) CNV	8	0	1
AMP PEAK 6(12P13.33) WILD-TYPE	4	28	9

Figure S3. Get High-res Image Gene #6: 'Amp Peak 6(12p13.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 7(12p12.1)' versus 'CN_CNMF'

P value = 0.000327 (Fisher's exact test), Q value = 0.081

Table S4. Gene #7: 'Amp Peak 7(12p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
AMP PEAK 7(12P12.1) CNV	7	1	1
AMP PEAK 7(12P12.1) WILD-TYPE	5	27	9

Figure S4. Get High-res Image Gene #7: 'Amp Peak 7(12p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 8(18q11.2)' versus 'CN_CNMF'

P value = 3.62e-05 (Fisher's exact test), Q value = 0.0097

Table S5. Gene #8: 'Amp Peak 8(18q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
AMP PEAK 8(18Q11.2) CNV	4	2	8
AMP PEAK 8(18Q11.2) WILD-TYPE	8	26	2

Figure S5. Get High-res Image Gene #8: 'Amp Peak 8(18q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 9(20q13.2)' versus 'CN_CNMF'

P value = 0.000157 (Fisher's exact test), Q value = 0.04

Table S6. Gene #9: 'Amp Peak 9(20q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
AMP PEAK 9(20Q13.2) CNV	9	3	2
AMP PEAK 9(20Q13.2) WILD-TYPE	3	25	8

Figure S6. Get High-res Image Gene #9: 'Amp Peak 9(20q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 2(1p21.2)' versus 'CN_CNMF'

P value = 5.64e-06 (Fisher's exact test), Q value = 0.0015

Table S7. Gene #13: 'Del Peak 2(1p21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
DEL PEAK 2(1P21.2) CNV	9	1	1
DEL PEAK 2(1P21.2) WILD-TYPE	3	27	9

Figure S7. Get High-res Image Gene #13: 'Del Peak 2(1p21.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 5(6p25.2)' versus 'CN_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.036

Table S8. Gene #16: 'Del Peak 5(6p25.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
DEL PEAK 5(6P25.2) CNV	10	5	6
DEL PEAK 5(6P25.2) WILD-TYPE	2	23	4

Figure S8. Get High-res Image Gene #16: 'Del Peak 5(6p25.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 5(6p25.2)' versus 'METHLYATION_CNMF'

P value = 4.59e-05 (Fisher's exact test), Q value = 0.012

Table S9. Gene #16: 'Del Peak 5(6p25.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	19	12
DEL PEAK 5(6P25.2) CNV	13	1	6
DEL PEAK 5(6P25.2) WILD-TYPE	5	18	6

Figure S9. Get High-res Image Gene #16: 'Del Peak 5(6p25.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 6(6p22.3)' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.075

Table S10. Gene #17: 'Del Peak 6(6p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
DEL PEAK 6(6P22.3) CNV	10	5	5
DEL PEAK 6(6P22.3) WILD-TYPE	2	23	5

Figure S10. Get High-res Image Gene #17: 'Del Peak 6(6p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 6(6p22.3)' versus 'METHLYATION_CNMF'

P value = 0.000136 (Fisher's exact test), Q value = 0.035

Table S11. Gene #17: 'Del Peak 6(6p22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	19	12
DEL PEAK 6(6P22.3) CNV	12	1	6
DEL PEAK 6(6P22.3) WILD-TYPE	6	18	6

Figure S11. Get High-res Image Gene #17: 'Del Peak 6(6p22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 7(6q22.33)' versus 'CN_CNMF'

P value = 3.74e-05 (Fisher's exact test), Q value = 0.01

Table S12. Gene #18: 'Del Peak 7(6q22.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
DEL PEAK 7(6Q22.33) CNV	11	7	8
DEL PEAK 7(6Q22.33) WILD-TYPE	1	21	2

Figure S12. Get High-res Image Gene #18: 'Del Peak 7(6q22.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 7(6q22.33)' versus 'METHLYATION_CNMF'

P value = 2.99e-06 (Fisher's exact test), Q value = 0.00083

Table S13. Gene #18: 'Del Peak 7(6q22.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	19	12
DEL PEAK 7(6Q22.33) CNV	16	2	7
DEL PEAK 7(6Q22.33) WILD-TYPE	2	17	5

Figure S13. Get High-res Image Gene #18: 'Del Peak 7(6q22.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 7(6q22.33)' versus 'MRNASEQ_CNMF'

P value = 0.000168 (Fisher's exact test), Q value = 0.043

Table S14. Gene #18: 'Del Peak 7(6q22.33)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	21	19
DEL PEAK 7(6Q22.33) CNV	16	3
DEL PEAK 7(6Q22.33) WILD-TYPE	5	16

Figure S14. Get High-res Image Gene #18: 'Del Peak 7(6q22.33)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 7(6q22.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.98e-05 (Fisher's exact test), Q value = 0.008

Table S15. Gene #18: 'Del Peak 7(6q22.33)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	17	19
DEL PEAK 7(6Q22.33) CNV	0	3	16
DEL PEAK 7(6Q22.33) WILD-TYPE	4	14	3

Figure S15. Get High-res Image Gene #18: 'Del Peak 7(6q22.33)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 7(6q22.33)' versus 'MIRSEQ_CNMF'

P value = 0.000423 (Chi-square test), Q value = 0.1

Table S16. Gene #18: 'Del Peak 7(6q22.33)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	9	5	9
DEL PEAK 7(6Q22.33) CNV	10	1	2	2	6
DEL PEAK 7(6Q22.33) WILD-TYPE	0	9	7	3	3

Figure S16. Get High-res Image Gene #18: 'Del Peak 7(6q22.33)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 7(6q22.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000497 (Fisher's exact test), Q value = 0.12

Table S17. Gene #18: 'Del Peak 7(6q22.33)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	9	16
DEL PEAK 7(6Q22.33) CNV	15	2	4
DEL PEAK 7(6Q22.33) WILD-TYPE	3	7	12

Figure S17. Get High-res Image Gene #18: 'Del Peak 7(6q22.33)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(6q22.33)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000203 (Fisher's exact test), Q value = 0.051

Table S18. Gene #18: 'Del Peak 7(6q22.33)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	22	21
DEL PEAK 7(6Q22.33) CNV	17	4
DEL PEAK 7(6Q22.33) WILD-TYPE	5	17

Figure S18. Get High-res Image Gene #18: 'Del Peak 7(6q22.33)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 7(6q22.33)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.16e-05 (Fisher's exact test), Q value = 0.0059

Table S19. Gene #18: 'Del Peak 7(6q22.33)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	9	16
DEL PEAK 7(6Q22.33) CNV	16	2	3
DEL PEAK 7(6Q22.33) WILD-TYPE	2	7	13

Figure S19. Get High-res Image Gene #18: 'Del Peak 7(6q22.33)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 9(8p23.1)' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.013

Table S20. Gene #20: 'Del Peak 9(8p23.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
DEL PEAK 9(8P23.1) CNV	9	2	4
DEL PEAK 9(8P23.1) WILD-TYPE	3	26	6

Figure S20. Get High-res Image Gene #20: 'Del Peak 9(8p23.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 9(8p23.1)' versus 'METHLYATION_CNMF'

P value = 0.000859 (Fisher's exact test), Q value = 0.21

Table S21. Gene #20: 'Del Peak 9(8p23.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	19	12
DEL PEAK 9(8P23.1) CNV	11	1	3
DEL PEAK 9(8P23.1) WILD-TYPE	7	18	9

Figure S21. Get High-res Image Gene #20: 'Del Peak 9(8p23.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 9(8p23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000786 (Fisher's exact test), Q value = 0.19

Table S22. Gene #20: 'Del Peak 9(8p23.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	17	19
DEL PEAK 9(8P23.1) CNV	0	1	11
DEL PEAK 9(8P23.1) WILD-TYPE	4	16	8

Figure S22. Get High-res Image Gene #20: 'Del Peak 9(8p23.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 9(8p23.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000196 (Fisher's exact test), Q value = 0.05

Table S23. Gene #20: 'Del Peak 9(8p23.1)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	22	21
DEL PEAK 9(8P23.1) CNV	13	1
DEL PEAK 9(8P23.1) WILD-TYPE	9	20

Figure S23. Get High-res Image Gene #20: 'Del Peak 9(8p23.1)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 11(9p21.3)' versus 'CN_CNMF'

P value = 2.64e-07 (Fisher's exact test), Q value = 7.4e-05

Table S24. Gene #22: 'Del Peak 11(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
DEL PEAK 11(9P21.3) CNV	12	8	10
DEL PEAK 11(9P21.3) WILD-TYPE	0	20	0

Figure S24. Get High-res Image Gene #22: 'Del Peak 11(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(9p21.3)' versus 'METHLYATION_CNMF'

P value = 4.84e-06 (Fisher's exact test), Q value = 0.0013

Table S25. Gene #22: 'Del Peak 11(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	19	12
DEL PEAK 11(9P21.3) CNV	18	5	6
DEL PEAK 11(9P21.3) WILD-TYPE	0	14	6

Figure S25. Get High-res Image Gene #22: 'Del Peak 11(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 11(9p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.17e-06 (Fisher's exact test), Q value = 0.0025

Table S26. Gene #22: 'Del Peak 11(9p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	17	19
DEL PEAK 11(9P21.3) CNV	0	4	17
DEL PEAK 11(9P21.3) WILD-TYPE	4	13	2

Figure S26. Get High-res Image Gene #22: 'Del Peak 11(9p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(9p21.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000203 (Fisher's exact test), Q value = 0.051

Table S27. Gene #22: 'Del Peak 11(9p21.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	22	21
DEL PEAK 11(9P21.3) CNV	18	5
DEL PEAK 11(9P21.3) WILD-TYPE	4	16

Figure S27. Get High-res Image Gene #22: 'Del Peak 11(9p21.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 11(9p21.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000234 (Fisher's exact test), Q value = 0.058

Table S28. Gene #22: 'Del Peak 11(9p21.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	9	16
DEL PEAK 11(9P21.3) CNV	16	2	5
DEL PEAK 11(9P21.3) WILD-TYPE	2	7	11

Figure S28. Get High-res Image Gene #22: 'Del Peak 11(9p21.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 13(10q23.2)' versus 'CN_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.041

Table S29. Gene #24: 'Del Peak 13(10q23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
DEL PEAK 13(10Q23.2) CNV	7	1	4
DEL PEAK 13(10Q23.2) WILD-TYPE	5	27	6

Figure S29. Get High-res Image Gene #24: 'Del Peak 13(10q23.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 16(12q12)' versus 'METHLYATION_CNMF'

P value = 3.27e-05 (Fisher's exact test), Q value = 0.0088

Table S30. Gene #27: 'Del Peak 16(12q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	19	12
DEL PEAK 16(12Q12) CNV	9	0	0
DEL PEAK 16(12Q12) WILD-TYPE	9	19	12

Figure S30. Get High-res Image Gene #27: 'Del Peak 16(12q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 17(12q24.32)' versus 'CN_CNMF'

P value = 0.000769 (Fisher's exact test), Q value = 0.19

Table S31. Gene #28: 'Del Peak 17(12q24.32)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
DEL PEAK 17(12Q24.32) CNV	9	4	3
DEL PEAK 17(12Q24.32) WILD-TYPE	3	24	7

Figure S31. Get High-res Image Gene #28: 'Del Peak 17(12q24.32)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 17(12q24.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000759 (Fisher's exact test), Q value = 0.18

Table S32. Gene #28: 'Del Peak 17(12q24.32)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	17	19
DEL PEAK 17(12Q24.32) CNV	1	0	10
DEL PEAK 17(12Q24.32) WILD-TYPE	3	17	9

Figure S32. Get High-res Image Gene #28: 'Del Peak 17(12q24.32)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(12q24.32)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.13e-05 (Fisher's exact test), Q value = 0.016

Table S33. Gene #28: 'Del Peak 17(12q24.32)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	22	21
DEL PEAK 17(12Q24.32) CNV	12	0
DEL PEAK 17(12Q24.32) WILD-TYPE	10	21

Figure S33. Get High-res Image Gene #28: 'Del Peak 17(12q24.32)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 18(15q15.1)' versus 'CN_CNMF'

P value = 7.9e-05 (Fisher's exact test), Q value = 0.021

Table S34. Gene #29: 'Del Peak 18(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
DEL PEAK 18(15Q15.1) CNV	6	0	4
DEL PEAK 18(15Q15.1) WILD-TYPE	6	28	6

Figure S34. Get High-res Image Gene #29: 'Del Peak 18(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 19(17p11.2)' versus 'CN_CNMF'

P value = 0.000191 (Fisher's exact test), Q value = 0.049

Table S35. Gene #30: 'Del Peak 19(17p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
DEL PEAK 19(17P11.2) CNV	9	4	6
DEL PEAK 19(17P11.2) WILD-TYPE	3	24	4

Figure S35. Get High-res Image Gene #30: 'Del Peak 19(17p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 19(17p11.2)' versus 'METHLYATION_CNMF'

P value = 2.77e-06 (Fisher's exact test), Q value = 0.00077

Table S36. Gene #30: 'Del Peak 19(17p11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	19	12
DEL PEAK 19(17P11.2) CNV	13	0	6
DEL PEAK 19(17P11.2) WILD-TYPE	5	19	6

Figure S36. Get High-res Image Gene #30: 'Del Peak 19(17p11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 19(17p11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.2e-05 (Fisher's exact test), Q value = 0.016

Table S37. Gene #30: 'Del Peak 19(17p11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	17	19
DEL PEAK 19(17P11.2) CNV	0	1	13
DEL PEAK 19(17P11.2) WILD-TYPE	4	16	6

Figure S37. Get High-res Image Gene #30: 'Del Peak 19(17p11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(17q23.2)' versus 'CN_CNMF'

P value = 0.000106 (Fisher's exact test), Q value = 0.028

Table S38. Gene #31: 'Del Peak 20(17q23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
DEL PEAK 20(17Q23.2) CNV	8	2	5
DEL PEAK 20(17Q23.2) WILD-TYPE	4	26	5

Figure S38. Get High-res Image Gene #31: 'Del Peak 20(17q23.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 20(17q23.2)' versus 'METHLYATION_CNMF'

P value = 0.000151 (Fisher's exact test), Q value = 0.039

Table S39. Gene #31: 'Del Peak 20(17q23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	19	12
DEL PEAK 20(17Q23.2) CNV	10	0	5
DEL PEAK 20(17Q23.2) WILD-TYPE	8	19	7

Figure S39. Get High-res Image Gene #31: 'Del Peak 20(17q23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 20(17q23.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000567 (Fisher's exact test), Q value = 0.14

Table S40. Gene #31: 'Del Peak 20(17q23.2)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	22	21
DEL PEAK 20(17Q23.2) CNV	12	1
DEL PEAK 20(17Q23.2) WILD-TYPE	10	20

Figure S40. Get High-res Image Gene #31: 'Del Peak 20(17q23.2)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 21(18q21.2)' versus 'CN_CNMF'

P value = 0.000918 (Fisher's exact test), Q value = 0.22

Table S41. Gene #32: 'Del Peak 21(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
DEL PEAK 21(18Q21.2) CNV	10	12	10
DEL PEAK 21(18Q21.2) WILD-TYPE	2	16	0

Figure S41. Get High-res Image Gene #32: 'Del Peak 21(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 24(Xq21.1)' versus 'CN_CNMF'

P value = 9.13e-06 (Fisher's exact test), Q value = 0.0025

Table S42. Gene #35: 'Del Peak 24(Xq21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	28	10
DEL PEAK 24(XQ21.1) CNV	7	0	0
DEL PEAK 24(XQ21.1) WILD-TYPE	5	28	10

Figure S42. Get High-res Image Gene #35: 'Del Peak 24(Xq21.1)' versus Molecular Subtype #1: 'CN_CNMF'

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 = PAAD-TP.transferedmergedcluster.txt
Number of patients = 50
Number of copy number variation regions = 35
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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