Correlation between copy number variation genes (focal events) and molecular subtypes

Pancreatic Adenocarcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

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 (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1SN07RH

Overview

Introduction

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

Summary

Testing the association between copy number variation 47 focal events and 8 molecular subtypes across 102 patients, 46 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_7q22.1 cnv correlated to 'CN_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_12p13.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_12p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_12p11.21 cnv correlated to 'CN_CNMF'.
amp_18q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_19q13.2 cnv correlated to 'CN_CNMF'.
amp_20q13.2 cnv correlated to 'CN_CNMF'.
del_1p36.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_1p21.2 cnv correlated to 'CN_CNMF'.
del_5q14.2 cnv correlated to 'CN_CNMF'.
del_6p25.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_7q36.1 cnv correlated to 'CN_CNMF'.
del_8p21.3 cnv correlated to 'CN_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.2 cnv correlated to 'CN_CNMF'.
del_12p12.3 cnv correlated to 'CN_CNMF'.
del_15q15.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_17q22 cnv correlated to 'CN_CNMF'.
del_18q21.2 cnv correlated to 'CN_CNMF'.
del_19p13.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_21q21.1 cnv correlated to 'CN_CNMF'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 47 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 46 significant findings detected.


		Clinical Features	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	Fisher's exact test	Fisher's exact test
del 9p21 3	67 (66%)	35	1e-05 (0.00376)	2e-05 (0.00726)	1e-05 (0.00376)	1e-05 (0.00376)	2e-05 (0.00726)	3e-05 (0.0107)	2e-05 (0.00726)	3e-05 (0.0107)
amp 18q11 2	34 (33%)	68	1e-05 (0.00376)	0.00014 (0.0482)	0.00032 (0.108)	0.00456 (1.00)	0.0001 (0.0347)	0.00385 (1.00)	3e-05 (0.0107)	0.00082 (0.27)
amp 12p13 33	16 (16%)	86	1e-05 (0.00376)	0.00018 (0.0616)	0.188 (1.00)	0.307 (1.00)	0.647 (1.00)	0.00051 (0.17)	0.0521 (1.00)	0.0828 (1.00)
amp 12p12 1	22 (22%)	80	1e-05 (0.00376)	2e-05 (0.00726)	0.0115 (1.00)	0.0341 (1.00)	0.145 (1.00)	5e-05 (0.0175)	0.00204 (0.647)	0.00658 (1.00)
del 1p36 11	35 (34%)	67	0.00024 (0.0818)	0.00052 (0.173)	6e-05 (0.021)	0.0302 (1.00)	0.0142 (1.00)	0.00415 (1.00)	0.00503 (1.00)	0.0114 (1.00)
del 22q13 31	35 (34%)	67	6e-05 (0.021)	0.0001 (0.0347)	0.00729 (1.00)	0.0232 (1.00)	0.188 (1.00)	0.00063 (0.209)	0.0148 (1.00)	0.0291 (1.00)
amp 8q24 21	42 (41%)	60	1e-05 (0.00376)	0.00028 (0.0949)	0.079 (1.00)	0.144 (1.00)	0.264 (1.00)	0.00462 (1.00)	0.0161 (1.00)	0.0133 (1.00)
del 6p25 2	42 (41%)	60	2e-05 (0.00726)	8e-05 (0.0278)	0.0395 (1.00)	0.123 (1.00)	0.1 (1.00)	0.00592 (1.00)	0.233 (1.00)	0.0214 (1.00)
del 15q15 1	23 (23%)	79	1e-05 (0.00376)	0.00026 (0.0884)	0.00461 (1.00)	0.00898 (1.00)	0.17 (1.00)	0.0168 (1.00)	0.0469 (1.00)	0.0148 (1.00)
del 19p13 3	20 (20%)	82	1e-05 (0.00376)	0.00116 (0.377)	0.0567 (1.00)	0.0349 (1.00)	0.716 (1.00)	0.00044 (0.147)	0.0585 (1.00)	0.199 (1.00)
amp 7q22 1	29 (28%)	73	1e-05 (0.00376)	0.0224 (1.00)	0.0449 (1.00)	0.147 (1.00)	0.333 (1.00)	0.179 (1.00)	0.00469 (1.00)	0.0231 (1.00)
amp 12p11 21	17 (17%)	85	1e-05 (0.00376)	0.0011 (0.36)	0.152 (1.00)	0.261 (1.00)	0.707 (1.00)	0.00725 (1.00)	0.0427 (1.00)	0.16 (1.00)
amp 19q13 2	26 (25%)	76	0.00048 (0.16)	0.00281 (0.885)	0.159 (1.00)	0.162 (1.00)	0.623 (1.00)	0.182 (1.00)	0.222 (1.00)	0.288 (1.00)
amp 20q13 2	31 (30%)	71	1e-05 (0.00376)	0.0192 (1.00)	0.217 (1.00)	0.615 (1.00)	0.657 (1.00)	0.00494 (1.00)	0.155 (1.00)	0.0496 (1.00)
del 1p21 2	23 (23%)	79	2e-05 (0.00726)	0.00592 (1.00)	0.0048 (1.00)	0.084 (1.00)	0.163 (1.00)	0.00457 (1.00)	0.0143 (1.00)	0.125 (1.00)
del 5q14 2	24 (24%)	78	3e-05 (0.0107)	0.0529 (1.00)	0.108 (1.00)	0.138 (1.00)	0.357 (1.00)	0.0392 (1.00)	0.0126 (1.00)	0.187 (1.00)
del 7q36 1	11 (11%)	91	0.00039 (0.131)	0.268 (1.00)	0.835 (1.00)	0.23 (1.00)	0.769 (1.00)	0.0203 (1.00)	1 (1.00)	0.826 (1.00)
del 8p21 3	32 (31%)	70	0.00016 (0.0549)	0.00176 (0.563)	0.00584 (1.00)	0.0728 (1.00)	0.0961 (1.00)	0.0013 (0.419)	0.00744 (1.00)	0.0374 (1.00)
del 10q23 2	19 (19%)	83	0.00031 (0.105)	0.102 (1.00)	0.0872 (1.00)	0.0385 (1.00)	0.677 (1.00)	0.0278 (1.00)	0.745 (1.00)	0.0213 (1.00)
del 12p12 3	15 (15%)	87	0.0001 (0.0347)	0.0024 (0.758)	0.106 (1.00)	0.11 (1.00)	0.0418 (1.00)	0.068 (1.00)	0.146 (1.00)	0.0377 (1.00)
del 17q22	28 (27%)	74	1e-05 (0.00376)	0.00085 (0.279)	0.0381 (1.00)	0.0391 (1.00)	0.138 (1.00)	0.00926 (1.00)	0.00994 (1.00)	0.0632 (1.00)
del 18q21 2	73 (72%)	29	4e-05 (0.0141)	0.0031 (0.973)	0.00639 (1.00)	0.0186 (1.00)	0.0369 (1.00)	0.0903 (1.00)	0.0123 (1.00)	0.0432 (1.00)
del 21q21 1	40 (39%)	62	3e-05 (0.0107)	0.0012 (0.389)	0.0131 (1.00)	0.0108 (1.00)	0.0796 (1.00)	0.00403 (1.00)	0.0213 (1.00)	0.0131 (1.00)
amp 1p34 2	7 (7%)	95	0.656 (1.00)	0.886 (1.00)	0.755 (1.00)	0.417 (1.00)	0.939 (1.00)	0.212 (1.00)	0.562 (1.00)	0.858 (1.00)
amp 1p12	16 (16%)	86	0.782 (1.00)	1 (1.00)	0.59 (1.00)	0.979 (1.00)	0.974 (1.00)	0.374 (1.00)	0.748 (1.00)	0.728 (1.00)
amp 6p21 31	7 (7%)	95	0.0709 (1.00)	0.342 (1.00)	0.303 (1.00)	0.623 (1.00)	0.704 (1.00)	0.0168 (1.00)	0.133 (1.00)	0.451 (1.00)
amp 9p13 3	12 (12%)	90	0.0451 (1.00)	0.175 (1.00)	0.11 (1.00)	0.56 (1.00)	0.442 (1.00)	0.152 (1.00)	0.32 (1.00)	0.0706 (1.00)
amp 11p11 2	12 (12%)	90	0.0215 (1.00)	0.174 (1.00)	0.454 (1.00)	0.786 (1.00)	0.694 (1.00)	0.196 (1.00)	0.359 (1.00)	0.396 (1.00)
amp 12q15	11 (11%)	91	0.0008 (0.264)	0.00135 (0.433)	0.0205 (1.00)	0.0477 (1.00)	0.197 (1.00)	0.00613 (1.00)	0.00828 (1.00)	0.0302 (1.00)
amp 17p11 2	5 (5%)	97	0.906 (1.00)	0.438 (1.00)	0.594 (1.00)	0.872 (1.00)	0.596 (1.00)	0.313 (1.00)	0.122 (1.00)	0.703 (1.00)
amp 17q21 32	11 (11%)	91	0.0412 (1.00)	0.494 (1.00)	0.267 (1.00)	0.562 (1.00)	1 (1.00)	0.208 (1.00)	1 (1.00)	0.643 (1.00)
amp xp22 11	5 (5%)	97	0.57 (1.00)	0.843 (1.00)	1 (1.00)	0.507 (1.00)	1 (1.00)	0.723 (1.00)	0.848 (1.00)	0.701 (1.00)
amp xq27 1	9 (9%)	93	0.106 (1.00)	1 (1.00)	0.436 (1.00)	0.572 (1.00)	0.92 (1.00)	0.562 (1.00)	0.901 (1.00)	0.521 (1.00)
del 1p36 32	26 (25%)	76	0.0019 (0.604)	0.0336 (1.00)	0.00183 (0.584)	0.0442 (1.00)	0.0662 (1.00)	0.036 (1.00)	0.0469 (1.00)	0.102 (1.00)
del 1q42 2	4 (4%)	98	0.0089 (1.00)	0.182 (1.00)	0.807 (1.00)	0.614 (1.00)	1 (1.00)	0.43 (1.00)	0.357 (1.00)	0.242 (1.00)
del 2p23 3	11 (11%)	91	0.032 (1.00)	0.27 (1.00)	0.196 (1.00)	0.131 (1.00)	0.227 (1.00)	0.354 (1.00)	0.322 (1.00)	0.11 (1.00)
del 2q37 3	4 (4%)	98	0.0397 (1.00)	0.18 (1.00)	0.182 (1.00)	0.401 (1.00)	0.446 (1.00)	0.3 (1.00)	0.0833 (1.00)	0.242 (1.00)
del 3p24 1	22 (22%)	80	0.00115 (0.375)	0.545 (1.00)	0.531 (1.00)	0.686 (1.00)	0.78 (1.00)	0.283 (1.00)	0.337 (1.00)	0.372 (1.00)
del 4q35 2	17 (17%)	85	0.392 (1.00)	0.397 (1.00)	0.521 (1.00)	0.78 (1.00)	1 (1.00)	0.717 (1.00)	0.783 (1.00)	0.585 (1.00)
del 8q12 1	9 (9%)	93	0.594 (1.00)	0.732 (1.00)	0.272 (1.00)	0.533 (1.00)	0.728 (1.00)	0.615 (1.00)	0.483 (1.00)	0.47 (1.00)
del 9q22 33	27 (26%)	75	0.0712 (1.00)	0.833 (1.00)	0.438 (1.00)	0.818 (1.00)	0.647 (1.00)	0.324 (1.00)	0.244 (1.00)	0.808 (1.00)
del 11p15 4	18 (18%)	84	0.0319 (1.00)	1 (1.00)	0.429 (1.00)	0.423 (1.00)	0.632 (1.00)	0.899 (1.00)	0.78 (1.00)	0.82 (1.00)
del 12q12	11 (11%)	91	0.00126 (0.407)	0.0111 (1.00)	0.183 (1.00)	0.0223 (1.00)	0.256 (1.00)	0.0653 (1.00)	0.268 (1.00)	0.0297 (1.00)
del 12q24 33	22 (22%)	80	0.00444 (1.00)	0.0401 (1.00)	0.00567 (1.00)	0.022 (1.00)	0.382 (1.00)	0.0273 (1.00)	0.276 (1.00)	0.0902 (1.00)
del 16q23 1	7 (7%)	95	0.13 (1.00)	0.888 (1.00)	0.476 (1.00)	0.526 (1.00)	0.882 (1.00)	0.443 (1.00)	0.661 (1.00)	1 (1.00)
del 18p11 32	38 (37%)	64	0.0586 (1.00)	0.386 (1.00)	0.893 (1.00)	0.784 (1.00)	0.843 (1.00)	0.404 (1.00)	0.963 (1.00)	0.673 (1.00)
del 19q13 41	11 (11%)	91	0.0414 (1.00)	0.496 (1.00)	0.387 (1.00)	0.265 (1.00)	0.553 (1.00)	0.388 (1.00)	0.915 (1.00)	0.905 (1.00)

'amp_7q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S1. Gene #4: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
AMP PEAK 4(7Q22.1) MUTATED	14	3	4	8
AMP PEAK 4(7Q22.1) WILD-TYPE	15	43	14	1

Figure S1. Get High-res Image Gene #4: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S2. Gene #5: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
AMP PEAK 5(8Q24.21) MUTATED	25	8	6	3
AMP PEAK 5(8Q24.21) WILD-TYPE	4	38	12	6

Figure S2. Get High-res Image Gene #5: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.095

Table S3. Gene #5: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	26	26
AMP PEAK 5(8Q24.21) MUTATED	30	6	5
AMP PEAK 5(8Q24.21) WILD-TYPE	19	20	21

Figure S3. Get High-res Image Gene #5: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S4. Gene #8: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
AMP PEAK 8(12P13.33) MUTATED	15	0	0	1
AMP PEAK 8(12P13.33) WILD-TYPE	14	46	18	8

Figure S4. Get High-res Image Gene #8: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.062

Table S5. Gene #8: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	26	26
AMP PEAK 8(12P13.33) MUTATED	15	1	0
AMP PEAK 8(12P13.33) WILD-TYPE	34	25	26

Figure S5. Get High-res Image Gene #8: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.17

Table S6. Gene #8: 'amp_12p13.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	17	20	18	8	20	12
AMP PEAK 8(12P13.33) MUTATED	7	1	0	4	2	1
AMP PEAK 8(12P13.33) WILD-TYPE	10	19	18	4	18	11

Figure S6. Get High-res Image Gene #8: 'amp_12p13.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S7. Gene #9: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
AMP PEAK 9(12P12.1) MUTATED	16	0	5	1
AMP PEAK 9(12P12.1) WILD-TYPE	13	46	13	8

Figure S7. Get High-res Image Gene #9: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0073

Table S8. Gene #9: 'amp_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	26	26
AMP PEAK 9(12P12.1) MUTATED	20	1	1
AMP PEAK 9(12P12.1) WILD-TYPE	29	25	25

Figure S8. Get High-res Image Gene #9: 'amp_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.018

Table S9. Gene #9: 'amp_12p12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	17	20	18	8	20	12
AMP PEAK 9(12P12.1) MUTATED	7	0	0	4	3	5
AMP PEAK 9(12P12.1) WILD-TYPE	10	20	18	4	17	7

Figure S9. Get High-res Image Gene #9: 'amp_12p12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_12p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S10. Gene #10: 'amp_12p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
AMP PEAK 10(12P11.21) MUTATED	14	0	3	0
AMP PEAK 10(12P11.21) WILD-TYPE	15	46	15	9

Figure S10. Get High-res Image Gene #10: 'amp_12p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S11. Gene #14: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
AMP PEAK 14(18Q11.2) MUTATED	11	4	16	3
AMP PEAK 14(18Q11.2) WILD-TYPE	18	42	2	6

Figure S11. Get High-res Image Gene #14: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.048

Table S12. Gene #14: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	26	26
AMP PEAK 14(18Q11.2) MUTATED	26	4	3
AMP PEAK 14(18Q11.2) WILD-TYPE	23	22	23

Figure S12. Get High-res Image Gene #14: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

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

Table S13. Gene #14: 'amp_18q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	26	23
AMP PEAK 14(18Q11.2) MUTATED	23	8	1
AMP PEAK 14(18Q11.2) WILD-TYPE	23	18	22

Figure S13. Get High-res Image Gene #14: 'amp_18q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.035

Table S14. Gene #14: 'amp_18q11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	25	13	20
AMP PEAK 14(18Q11.2) MUTATED	22	7	1	2
AMP PEAK 14(18Q11.2) WILD-TYPE	15	18	12	18

Figure S14. Get High-res Image Gene #14: 'amp_18q11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.011

Table S15. Gene #14: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	23	31
AMP PEAK 14(18Q11.2) MUTATED	24	5	3
AMP PEAK 14(18Q11.2) WILD-TYPE	17	18	28

Figure S15. Get High-res Image Gene #14: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.2' versus 'CN_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.16

Table S16. Gene #15: 'amp_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
AMP PEAK 15(19Q13.2) MUTATED	14	4	4	4
AMP PEAK 15(19Q13.2) WILD-TYPE	15	42	14	5

Figure S16. Get High-res Image Gene #15: 'amp_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S17. Gene #16: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
AMP PEAK 16(20Q13.2) MUTATED	19	6	1	5
AMP PEAK 16(20Q13.2) WILD-TYPE	10	40	17	4

Figure S17. Get High-res Image Gene #16: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.082

Table S18. Gene #20: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
DEL PEAK 2(1P36.11) MUTATED	18	7	8	2
DEL PEAK 2(1P36.11) WILD-TYPE	11	39	10	7

Figure S18. Get High-res Image Gene #20: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.17

Table S19. Gene #20: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	26	26
DEL PEAK 2(1P36.11) MUTATED	25	8	2
DEL PEAK 2(1P36.11) WILD-TYPE	24	18	24

Figure S19. Get High-res Image Gene #20: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.021

Table S20. Gene #20: 'del_1p36.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	26	23
DEL PEAK 2(1P36.11) MUTATED	18	13	0
DEL PEAK 2(1P36.11) WILD-TYPE	28	13	23

Figure S20. Get High-res Image Gene #20: 'del_1p36.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p21.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0073

Table S21. Gene #21: 'del_1p21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
DEL PEAK 3(1P21.2) MUTATED	16	4	3	0
DEL PEAK 3(1P21.2) WILD-TYPE	13	42	15	9

Figure S21. Get High-res Image Gene #21: 'del_1p21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q14.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.011

Table S22. Gene #27: 'del_5q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
DEL PEAK 9(5Q14.2) MUTATED	16	3	4	1
DEL PEAK 9(5Q14.2) WILD-TYPE	13	43	14	8

Figure S22. Get High-res Image Gene #27: 'del_5q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0073

Table S23. Gene #28: 'del_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
DEL PEAK 10(6P25.2) MUTATED	21	7	7	7
DEL PEAK 10(6P25.2) WILD-TYPE	8	39	11	2

Figure S23. Get High-res Image Gene #28: 'del_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.2' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.028

Table S24. Gene #28: 'del_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	26	26
DEL PEAK 10(6P25.2) MUTATED	31	4	6
DEL PEAK 10(6P25.2) WILD-TYPE	18	22	20

Figure S24. Get High-res Image Gene #28: 'del_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.1' versus 'CN_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.13

Table S25. Gene #29: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
DEL PEAK 11(7Q36.1) MUTATED	8	0	1	2
DEL PEAK 11(7Q36.1) WILD-TYPE	21	46	17	7

Figure S25. Get High-res Image Gene #29: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p21.3' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.055

Table S26. Gene #30: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
DEL PEAK 12(8P21.3) MUTATED	18	6	6	2
DEL PEAK 12(8P21.3) WILD-TYPE	11	40	12	7

Figure S26. Get High-res Image Gene #30: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S27. Gene #32: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
DEL PEAK 14(9P21.3) MUTATED	27	15	17	8
DEL PEAK 14(9P21.3) WILD-TYPE	2	31	1	1

Figure S27. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0073

Table S28. Gene #32: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	26	26
DEL PEAK 14(9P21.3) MUTATED	43	10	13
DEL PEAK 14(9P21.3) WILD-TYPE	6	16	13

Figure S28. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S29. Gene #32: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	46	26	23
DEL PEAK 14(9P21.3) MUTATED	39	15	6
DEL PEAK 14(9P21.3) WILD-TYPE	7	11	17

Figure S29. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S30. Gene #32: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	27	13	14	12	22	7
DEL PEAK 14(9P21.3) MUTATED	26	10	4	7	10	3
DEL PEAK 14(9P21.3) WILD-TYPE	1	3	10	5	12	4

Figure S30. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0073

Table S31. Gene #32: 'del_9p21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	25	13	20
DEL PEAK 14(9P21.3) MUTATED	34	12	4	10
DEL PEAK 14(9P21.3) WILD-TYPE	3	13	9	10

Figure S31. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.011

Table S32. Gene #32: 'del_9p21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	17	20	18	8	20	12
DEL PEAK 14(9P21.3) MUTATED	17	8	5	6	14	10
DEL PEAK 14(9P21.3) WILD-TYPE	0	12	13	2	6	2

Figure S32. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0073

Table S33. Gene #32: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	23	31
DEL PEAK 14(9P21.3) MUTATED	36	13	11
DEL PEAK 14(9P21.3) WILD-TYPE	5	10	20

Figure S33. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.011

Table S34. Gene #32: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	28	19
DEL PEAK 14(9P21.3) MUTATED	41	13	6
DEL PEAK 14(9P21.3) WILD-TYPE	7	15	13

Figure S34. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.2' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.1

Table S35. Gene #34: 'del_10q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
DEL PEAK 16(10Q23.2) MUTATED	12	2	2	3
DEL PEAK 16(10Q23.2) WILD-TYPE	17	44	16	6

Figure S35. Get High-res Image Gene #34: 'del_10q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p12.3' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.035

Table S36. Gene #36: 'del_12p12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
DEL PEAK 18(12P12.3) MUTATED	6	0	6	3
DEL PEAK 18(12P12.3) WILD-TYPE	23	46	12	6

Figure S36. Get High-res Image Gene #36: 'del_12p12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S37. Gene #39: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
DEL PEAK 21(15Q15.1) MUTATED	15	1	4	3
DEL PEAK 21(15Q15.1) WILD-TYPE	14	45	14	6

Figure S37. Get High-res Image Gene #39: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.088

Table S38. Gene #39: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	26	26
DEL PEAK 21(15Q15.1) MUTATED	19	1	2
DEL PEAK 21(15Q15.1) WILD-TYPE	30	25	24

Figure S38. Get High-res Image Gene #39: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S39. Gene #41: 'del_17q22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
DEL PEAK 23(17Q22) MUTATED	18	1	5	4
DEL PEAK 23(17Q22) WILD-TYPE	11	45	13	5

Figure S39. Get High-res Image Gene #41: 'del_17q22' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S40. Gene #43: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
DEL PEAK 25(18Q21.2) MUTATED	25	23	18	7
DEL PEAK 25(18Q21.2) WILD-TYPE	4	23	0	2

Figure S40. Get High-res Image Gene #43: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0038

Table S41. Gene #44: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
DEL PEAK 26(19P13.3) MUTATED	15	1	2	2
DEL PEAK 26(19P13.3) WILD-TYPE	14	45	16	7

Figure S41. Get High-res Image Gene #44: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.15

Table S42. Gene #44: 'del_19p13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	17	20	18	8	20	12
DEL PEAK 26(19P13.3) MUTATED	8	1	1	5	3	1
DEL PEAK 26(19P13.3) WILD-TYPE	9	19	17	3	17	11

Figure S42. Get High-res Image Gene #44: 'del_19p13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_21q21.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.011

Table S43. Gene #46: 'del_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
DEL PEAK 28(21Q21.1) MUTATED	18	7	9	6
DEL PEAK 28(21Q21.1) WILD-TYPE	11	39	9	3

Figure S43. Get High-res Image Gene #46: 'del_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.021

Table S44. Gene #47: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	46	18	9
DEL PEAK 29(22Q13.31) MUTATED	18	5	9	3
DEL PEAK 29(22Q13.31) WILD-TYPE	11	41	9	6

Figure S44. Get High-res Image Gene #47: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.035

Table S45. Gene #47: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	26	26
DEL PEAK 29(22Q13.31) MUTATED	27	3	5
DEL PEAK 29(22Q13.31) WILD-TYPE	22	23	21

Figure S45. Get High-res Image Gene #47: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.21

Table S46. Gene #47: 'del_22q13.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	17	20	18	8	20	12
DEL PEAK 29(22Q13.31) MUTATED	9	5	1	5	4	8
DEL PEAK 29(22Q13.31) WILD-TYPE	8	15	17	3	16	4

Figure S46. Get High-res Image Gene #47: 'del_22q13.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = PAAD-TP.transferedmergedcluster.txt
Number of patients = 102
Number of significantly focal cnvs = 47
Number of molecular subtypes = 8
Exclude genes 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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] 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)

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