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

Pancreatic Adenocarcinoma (Primary solid tumor)

15 January 2014 | analyses__2014_01_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/C11G0JRP

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 40 focal events and 8 molecular subtypes across 81 patients, 59 significant findings detected with P value < 0.05 and Q value < 0.25.

3p cnv correlated to 'CN_CNMF'.
3q cnv correlated to 'METHLYATION_CNMF'.
6p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
6q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8p cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8q cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
9p cnv correlated to 'CN_CNMF'.
10p cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10q cnv correlated to 'CN_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12p cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12q cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
16p cnv correlated to 'CN_CNMF'.
17p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17q cnv correlated to 'CN_CNMF'.
18q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
20p cnv correlated to 'CN_CNMF'.
21q cnv correlated to 'CN_CNMF'.
22q cnv correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 40 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, 59 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
6q	35 (43%)	46	5.19e-05 (0.0157)	1.49e-07 (4.75e-05)	0.000314 (0.0898)	4.62e-07 (0.000146)	7.27e-05 (0.0219)	8.59e-06 (0.00267)	1.11e-05 (0.00344)	4.28e-05 (0.0131)
17p	34 (42%)	47	7.34e-10 (2.34e-07)	1.52e-11 (4.87e-09)	0.000711 (0.194)	4.46e-05 (0.0135)	0.000209 (0.0614)	0.000326 (0.0922)	1.56e-05 (0.00481)	0.000123 (0.0365)
8q	22 (27%)	59	0.00243 (0.578)	0.000755 (0.204)	4.42e-05 (0.0135)	8.83e-05 (0.0265)	0.000555 (0.154)	0.000982 (0.255)	0.000507 (0.142)	0.000654 (0.18)
12p	16 (20%)	65	8.07e-06 (0.00253)	0.00229 (0.551)	0.000143 (0.0423)	0.000315 (0.0898)	0.000263 (0.0761)	0.0019 (0.47)	0.000232 (0.0676)	0.000843 (0.225)
6p	29 (36%)	52	2.07e-05 (0.00637)	4.1e-06 (0.00129)	0.000763 (0.205)	0.00708 (1.00)	0.00832 (1.00)	0.000268 (0.0772)	0.000315 (0.0898)	0.00107 (0.275)
8p	21 (26%)	60	0.00678 (1.00)	0.000993 (0.256)	4.42e-05 (0.0135)	8.83e-05 (0.0265)	0.000555 (0.154)	0.000982 (0.255)	0.000507 (0.142)	0.000654 (0.18)
10p	15 (19%)	66	0.000841 (0.225)	0.0344 (1.00)	0.019 (1.00)	0.000786 (0.211)	0.00192 (0.471)	0.000862 (0.228)	0.000212 (0.0619)	0.000554 (0.154)
10q	16 (20%)	65	8.07e-06 (0.00253)	0.0282 (1.00)	0.0296 (1.00)	0.00272 (0.634)	0.00294 (0.677)	0.0019 (0.47)	0.000232 (0.0676)	0.000843 (0.225)
12q	16 (20%)	65	2.99e-06 (0.000942)	0.00229 (0.551)	0.000899 (0.236)	0.00384 (0.867)	0.00107 (0.275)	0.00564 (1.00)	0.000448 (0.126)	0.00397 (0.889)
18q	47 (58%)	34	9.76e-05 (0.0291)	0.00048 (0.135)	0.0577 (1.00)	0.0298 (1.00)	0.08 (1.00)	0.0181 (1.00)	0.00999 (1.00)	0.0405 (1.00)
3p	16 (20%)	65	0.000191 (0.0561)	0.0114 (1.00)	0.0248 (1.00)	0.0619 (1.00)	0.0624 (1.00)	0.215 (1.00)	0.0656 (1.00)	0.141 (1.00)
3q	15 (19%)	66	0.00428 (0.946)	0.000936 (0.245)	0.0121 (1.00)	0.00942 (1.00)	0.0421 (1.00)	0.118 (1.00)	0.0462 (1.00)	0.0926 (1.00)
9p	37 (46%)	44	2.83e-05 (0.00868)	0.00662 (1.00)	0.0403 (1.00)	0.00328 (0.749)	0.0484 (1.00)	0.116 (1.00)	0.04 (1.00)	0.0766 (1.00)
16p	10 (12%)	71	0.000738 (0.2)	0.00247 (0.585)	0.0244 (1.00)	0.049 (1.00)	0.0436 (1.00)	0.0286 (1.00)	0.00327 (0.749)	0.0172 (1.00)
17q	15 (19%)	66	0.000309 (0.0887)	0.00177 (0.441)	0.0121 (1.00)	0.0214 (1.00)	0.0421 (1.00)	0.118 (1.00)	0.0179 (1.00)	0.0926 (1.00)
20p	20 (25%)	61	0.00073 (0.199)	0.00252 (0.595)	0.0424 (1.00)	0.0151 (1.00)	0.00998 (1.00)	0.0253 (1.00)	0.0099 (1.00)	0.0161 (1.00)
21q	29 (36%)	52	6.32e-07 (2e-04)	0.00241 (0.576)	0.0606 (1.00)	0.00815 (1.00)	0.0149 (1.00)	0.135 (1.00)	0.043 (1.00)	0.0816 (1.00)
22q	20 (25%)	61	0.000177 (0.0523)	0.0178 (1.00)	0.0248 (1.00)	0.0619 (1.00)	0.124 (1.00)	0.331 (1.00)	0.231 (1.00)	0.256 (1.00)
1p	17 (21%)	64	0.00797 (1.00)	0.00209 (0.51)	0.234 (1.00)	0.245 (1.00)	0.306 (1.00)	0.731 (1.00)	0.584 (1.00)	0.668 (1.00)
1q	22 (27%)	59	0.0685 (1.00)	0.0121 (1.00)	0.0602 (1.00)	0.117 (1.00)	0.159 (1.00)	0.614 (1.00)	0.496 (1.00)	0.53 (1.00)
2p	12 (15%)	69	0.00401 (0.894)	0.0221 (1.00)	0.26 (1.00)	0.0209 (1.00)	0.0772 (1.00)	0.205 (1.00)	0.0435 (1.00)	0.185 (1.00)
2q	8 (10%)	73	0.0084 (1.00)	0.00941 (1.00)	0.00617 (1.00)	0.00169 (0.422)	0.0225 (1.00)	0.138 (1.00)	0.0383 (1.00)	0.092 (1.00)
4p	12 (15%)	69	0.013 (1.00)	0.112 (1.00)	0.421 (1.00)	0.0513 (1.00)	0.215 (1.00)	0.561 (1.00)	0.136 (1.00)	0.453 (1.00)
4q	11 (14%)	70	0.0266 (1.00)	0.0353 (1.00)	0.349 (1.00)	0.134 (1.00)	0.321 (1.00)	0.38 (1.00)	0.606 (1.00)	0.425 (1.00)
5p	12 (15%)	69	0.00154 (0.389)	0.0221 (1.00)	0.0587 (1.00)	0.0562 (1.00)	0.108 (1.00)	0.255 (1.00)	0.151 (1.00)	0.195 (1.00)
5q	12 (15%)	69	0.00154 (0.389)	0.0221 (1.00)	0.0587 (1.00)	0.0562 (1.00)	0.0436 (1.00)	0.149 (1.00)	0.0607 (1.00)	0.122 (1.00)
7p	21 (26%)	60	0.0207 (1.00)	0.00155 (0.39)	0.0331 (1.00)	0.0363 (1.00)	0.0158 (1.00)	0.174 (1.00)	0.0383 (1.00)	0.139 (1.00)
7q	19 (23%)	62	0.0639 (1.00)	0.0053 (1.00)	0.0331 (1.00)	0.0363 (1.00)	0.0158 (1.00)	0.174 (1.00)	0.0383 (1.00)	0.139 (1.00)
9q	24 (30%)	57	0.0848 (1.00)	0.243 (1.00)	0.479 (1.00)	1 (1.00)	0.482 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
11p	13 (16%)	68	0.00271 (0.634)	0.0885 (1.00)	0.263 (1.00)	0.777 (1.00)	0.295 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
11q	13 (16%)	68	0.0283 (1.00)	0.175 (1.00)	0.487 (1.00)	0.559 (1.00)	0.816 (1.00)	0.597 (1.00)	0.584 (1.00)	0.608 (1.00)
13q	16 (20%)	65	0.0293 (1.00)	1 (1.00)	0.613 (1.00)	0.545 (1.00)	0.434 (1.00)	0.762 (1.00)	0.475 (1.00)	0.641 (1.00)
14q	13 (16%)	68	0.131 (1.00)	0.0452 (1.00)	0.125 (1.00)	0.196 (1.00)	0.477 (1.00)	0.331 (1.00)	0.49 (1.00)	0.336 (1.00)
15q	17 (21%)	64	0.00367 (0.832)	0.00138 (0.349)	0.00293 (0.677)	0.0018 (0.447)	0.00105 (0.271)	0.00621 (1.00)	0.00417 (0.926)	0.00387 (0.871)
16q	11 (14%)	70	0.000967 (0.252)	0.00258 (0.606)	0.00999 (1.00)	0.133 (1.00)	0.0256 (1.00)	0.00895 (1.00)	0.00227 (0.549)	0.0089 (1.00)
18p	39 (48%)	42	0.131 (1.00)	0.00509 (1.00)	0.536 (1.00)	0.373 (1.00)	0.438 (1.00)	0.203 (1.00)	0.0966 (1.00)	0.308 (1.00)
19p	11 (14%)	70	0.0124 (1.00)	0.197 (1.00)	0.0296 (1.00)	0.00272 (0.634)	0.00844 (1.00)	0.0291 (1.00)	0.0118 (1.00)	0.0253 (1.00)
19q	14 (17%)	67	0.0976 (1.00)	0.175 (1.00)	0.0939 (1.00)	0.00914 (1.00)	0.034 (1.00)	0.0135 (1.00)	0.037 (1.00)	0.0921 (1.00)
20q	18 (22%)	63	0.00223 (0.541)	0.0349 (1.00)	0.12 (1.00)	0.00942 (1.00)	0.0194 (1.00)	0.0529 (1.00)	0.00922 (1.00)	0.04 (1.00)
xq	8 (10%)	73	0.134 (1.00)	0.509 (1.00)	0.391 (1.00)	0.615 (1.00)	0.204 (1.00)	1 (1.00)	0.248 (1.00)	0.342 (1.00)

'3p' versus 'CN_CNMF'

P value = 0.000191 (Fisher's exact test), Q value = 0.056

Table S1. Gene #5: '3p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	42	19
3P MUTATED	3	3	10
3P WILD-TYPE	17	39	9

Figure S1. Get High-res Image Gene #5: '3p' versus Molecular Subtype #1: 'CN_CNMF'

'3q' versus 'METHLYATION_CNMF'

P value = 0.000936 (Fisher's exact test), Q value = 0.25

Table S2. Gene #6: '3q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	34	19
3Q MUTATED	6	1	8
3Q WILD-TYPE	21	33	11

Figure S2. Get High-res Image Gene #6: '3q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p' versus 'CN_CNMF'

P value = 2.07e-05 (Fisher's exact test), Q value = 0.0064

Table S3. Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	42	19
6P MUTATED	9	6	14
6P WILD-TYPE	11	36	5

Figure S3. Get High-res Image Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

'6p' versus 'METHLYATION_CNMF'

P value = 4.1e-06 (Fisher's exact test), Q value = 0.0013

Table S4. Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	34	19
6P MUTATED	15	2	11
6P WILD-TYPE	12	32	8

Figure S4. Get High-res Image Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p' versus 'MRNASEQ_CNMF'

P value = 0.000763 (Fisher's exact test), Q value = 0.21

Table S5. Gene #11: '6p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	12	12	10
6P MUTATED	13	2	2	0
6P WILD-TYPE	8	10	10	10

Figure S5. Get High-res Image Gene #11: '6p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000268 (Fisher's exact test), Q value = 0.077

Table S6. Gene #11: '6p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	20	27
6P MUTATED	1	2	16
6P WILD-TYPE	10	18	11

Figure S6. Get High-res Image Gene #11: '6p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000315 (Fisher's exact test), Q value = 0.09

Table S7. Gene #11: '6p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	10	23
6P MUTATED	15	0	4
6P WILD-TYPE	10	10	19

Figure S7. Get High-res Image Gene #11: '6p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q' versus 'CN_CNMF'

P value = 5.19e-05 (Fisher's exact test), Q value = 0.016

Table S8. Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	42	19
6Q MUTATED	11	9	15
6Q WILD-TYPE	9	33	4

Figure S8. Get High-res Image Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

'6q' versus 'METHLYATION_CNMF'

P value = 1.49e-07 (Fisher's exact test), Q value = 4.8e-05

Table S9. Gene #12: '6q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	34	19
6Q MUTATED	20	3	11
6Q WILD-TYPE	7	31	8

Figure S9. Get High-res Image Gene #12: '6q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q' versus 'MRNASEQ_CNMF'

P value = 0.000314 (Fisher's exact test), Q value = 0.09

Table S10. Gene #12: '6q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	12	12	10
6Q MUTATED	16	2	2	2
6Q WILD-TYPE	5	10	10	8

Figure S10. Get High-res Image Gene #12: '6q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.62e-07 (Fisher's exact test), Q value = 0.00015

Table S11. Gene #12: '6q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	22	28
6Q MUTATED	0	18	4
6Q WILD-TYPE	5	4	24

Figure S11. Get High-res Image Gene #12: '6q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q' versus 'MIRSEQ_CNMF'

P value = 7.27e-05 (Fisher's exact test), Q value = 0.022

Table S12. Gene #12: '6q' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	11	18
6Q MUTATED	20	2	2
6Q WILD-TYPE	9	9	16

Figure S12. Get High-res Image Gene #12: '6q' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.59e-06 (Fisher's exact test), Q value = 0.0027

Table S13. Gene #12: '6q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	20	27
6Q MUTATED	1	3	20
6Q WILD-TYPE	10	17	7

Figure S13. Get High-res Image Gene #12: '6q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0034

Table S14. Gene #12: '6q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	10	23
6Q MUTATED	19	1	4
6Q WILD-TYPE	6	9	19

Figure S14. Get High-res Image Gene #12: '6q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.28e-05 (Fisher's exact test), Q value = 0.013

Table S15. Gene #12: '6q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	26	20
6Q MUTATED	2	19	3
6Q WILD-TYPE	10	7	17

Figure S15. Get High-res Image Gene #12: '6q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p' versus 'MRNASEQ_CNMF'

P value = 4.42e-05 (Fisher's exact test), Q value = 0.013

Table S16. Gene #15: '8p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	12	12	10
8P MUTATED	13	0	2	0
8P WILD-TYPE	8	12	10	10

Figure S16. Get High-res Image Gene #15: '8p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.83e-05 (Fisher's exact test), Q value = 0.026

Table S17. Gene #15: '8p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	22	28
8P MUTATED	0	13	2
8P WILD-TYPE	5	9	26

Figure S17. Get High-res Image Gene #15: '8p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p' versus 'MIRSEQ_CNMF'

P value = 0.000555 (Fisher's exact test), Q value = 0.15

Table S18. Gene #15: '8p' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	11	18
8P MUTATED	15	0	2
8P WILD-TYPE	14	11	16

Figure S18. Get High-res Image Gene #15: '8p' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000507 (Fisher's exact test), Q value = 0.14

Table S19. Gene #15: '8p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	10	23
8P MUTATED	14	1	2
8P WILD-TYPE	11	9	21

Figure S19. Get High-res Image Gene #15: '8p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000654 (Fisher's exact test), Q value = 0.18

Table S20. Gene #15: '8p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	26	20
8P MUTATED	2	14	1
8P WILD-TYPE	10	12	19

Figure S20. Get High-res Image Gene #15: '8p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q' versus 'METHLYATION_CNMF'

P value = 0.000755 (Fisher's exact test), Q value = 0.2

Table S21. Gene #16: '8q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	34	19
8Q MUTATED	12	2	7
8Q WILD-TYPE	15	32	12

Figure S21. Get High-res Image Gene #16: '8q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q' versus 'MRNASEQ_CNMF'

P value = 4.42e-05 (Fisher's exact test), Q value = 0.013

Table S22. Gene #16: '8q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	12	12	10
8Q MUTATED	13	0	2	0
8Q WILD-TYPE	8	12	10	10

Figure S22. Get High-res Image Gene #16: '8q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.83e-05 (Fisher's exact test), Q value = 0.026

Table S23. Gene #16: '8q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	22	28
8Q MUTATED	0	13	2
8Q WILD-TYPE	5	9	26

Figure S23. Get High-res Image Gene #16: '8q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q' versus 'MIRSEQ_CNMF'

P value = 0.000555 (Fisher's exact test), Q value = 0.15

Table S24. Gene #16: '8q' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	11	18
8Q MUTATED	15	0	2
8Q WILD-TYPE	14	11	16

Figure S24. Get High-res Image Gene #16: '8q' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000507 (Fisher's exact test), Q value = 0.14

Table S25. Gene #16: '8q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	10	23
8Q MUTATED	14	1	2
8Q WILD-TYPE	11	9	21

Figure S25. Get High-res Image Gene #16: '8q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000654 (Fisher's exact test), Q value = 0.18

Table S26. Gene #16: '8q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	26	20
8Q MUTATED	2	14	1
8Q WILD-TYPE	10	12	19

Figure S26. Get High-res Image Gene #16: '8q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p' versus 'CN_CNMF'

P value = 2.83e-05 (Fisher's exact test), Q value = 0.0087

Table S27. Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	42	19
9P MUTATED	11	10	16
9P WILD-TYPE	9	32	3

Figure S27. Get High-res Image Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'CN_CNMF'

P value = 0.000841 (Fisher's exact test), Q value = 0.22

Table S28. Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	42	19
10P MUTATED	5	2	8
10P WILD-TYPE	15	40	11

Figure S28. Get High-res Image Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000786 (Fisher's exact test), Q value = 0.21

Table S29. Gene #19: '10p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	22	28
10P MUTATED	0	8	0
10P WILD-TYPE	5	14	28

Figure S29. Get High-res Image Gene #19: '10p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000862 (Fisher's exact test), Q value = 0.23

Table S30. Gene #19: '10p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	20	27
10P MUTATED	0	0	10
10P WILD-TYPE	11	20	17

Figure S30. Get High-res Image Gene #19: '10p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000212 (Fisher's exact test), Q value = 0.062

Table S31. Gene #19: '10p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	10	23
10P MUTATED	10	0	0
10P WILD-TYPE	15	10	23

Figure S31. Get High-res Image Gene #19: '10p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'10p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000554 (Fisher's exact test), Q value = 0.15

Table S32. Gene #19: '10p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	26	20
10P MUTATED	0	10	0
10P WILD-TYPE	12	16	20

Figure S32. Get High-res Image Gene #19: '10p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q' versus 'CN_CNMF'

P value = 8.07e-06 (Fisher's exact test), Q value = 0.0025

Table S33. Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	42	19
10Q MUTATED	5	1	10
10Q WILD-TYPE	15	41	9

Figure S33. Get High-res Image Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

'10q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000232 (Fisher's exact test), Q value = 0.068

Table S34. Gene #20: '10q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	10	23
10Q MUTATED	11	1	0
10Q WILD-TYPE	14	9	23

Figure S34. Get High-res Image Gene #20: '10q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'10q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000843 (Fisher's exact test), Q value = 0.22

Table S35. Gene #20: '10q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	26	20
10Q MUTATED	0	11	1
10Q WILD-TYPE	12	15	19

Figure S35. Get High-res Image Gene #20: '10q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p' versus 'CN_CNMF'

P value = 8.07e-06 (Fisher's exact test), Q value = 0.0025

Table S36. Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	42	19
12P MUTATED	5	1	10
12P WILD-TYPE	15	41	9

Figure S36. Get High-res Image Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

'12p' versus 'MRNASEQ_CNMF'

P value = 0.000143 (Fisher's exact test), Q value = 0.042

Table S37. Gene #23: '12p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	12	12	10
12P MUTATED	10	0	0	0
12P WILD-TYPE	11	12	12	10

Figure S37. Get High-res Image Gene #23: '12p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000315 (Fisher's exact test), Q value = 0.09

Table S38. Gene #23: '12p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	22	28
12P MUTATED	1	9	0
12P WILD-TYPE	4	13	28

Figure S38. Get High-res Image Gene #23: '12p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12p' versus 'MIRSEQ_CNMF'

P value = 0.000263 (Fisher's exact test), Q value = 0.076

Table S39. Gene #23: '12p' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	11	18
12P MUTATED	12	0	0
12P WILD-TYPE	17	11	18

Figure S39. Get High-res Image Gene #23: '12p' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'12p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000232 (Fisher's exact test), Q value = 0.068

Table S40. Gene #23: '12p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	10	23
12P MUTATED	11	1	0
12P WILD-TYPE	14	9	23

Figure S40. Get High-res Image Gene #23: '12p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'12p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000843 (Fisher's exact test), Q value = 0.22

Table S41. Gene #23: '12p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	26	20
12P MUTATED	0	11	1
12P WILD-TYPE	12	15	19

Figure S41. Get High-res Image Gene #23: '12p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q' versus 'CN_CNMF'

P value = 2.99e-06 (Fisher's exact test), Q value = 0.00094

Table S42. Gene #24: '12q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	42	19
12Q MUTATED	4	1	11
12Q WILD-TYPE	16	41	8

Figure S42. Get High-res Image Gene #24: '12q' versus Molecular Subtype #1: 'CN_CNMF'

'12q' versus 'MRNASEQ_CNMF'

P value = 0.000899 (Fisher's exact test), Q value = 0.24

Table S43. Gene #24: '12q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	12	12	10
12Q MUTATED	10	1	0	0
12Q WILD-TYPE	11	11	12	10

Figure S43. Get High-res Image Gene #24: '12q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000448 (Fisher's exact test), Q value = 0.13

Table S44. Gene #24: '12q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	10	23
12Q MUTATED	11	2	0
12Q WILD-TYPE	14	8	23

Figure S44. Get High-res Image Gene #24: '12q' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16p' versus 'CN_CNMF'

P value = 0.000738 (Fisher's exact test), Q value = 0.2

Table S45. Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	42	19
16P MUTATED	2	1	7
16P WILD-TYPE	18	41	12

Figure S45. Get High-res Image Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

'17p' versus 'CN_CNMF'

P value = 7.34e-10 (Fisher's exact test), Q value = 2.3e-07

Table S46. Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	42	19
17P MUTATED	14	4	16
17P WILD-TYPE	6	38	3

Figure S46. Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

'17p' versus 'METHLYATION_CNMF'

P value = 1.52e-11 (Fisher's exact test), Q value = 4.9e-09

Table S47. Gene #30: '17p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	34	19
17P MUTATED	23	1	10
17P WILD-TYPE	4	33	9

Figure S47. Get High-res Image Gene #30: '17p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p' versus 'MRNASEQ_CNMF'

P value = 0.000711 (Fisher's exact test), Q value = 0.19

Table S48. Gene #30: '17p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	12	12	10
17P MUTATED	15	3	1	2
17P WILD-TYPE	6	9	11	8

Figure S48. Get High-res Image Gene #30: '17p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.46e-05 (Fisher's exact test), Q value = 0.014

Table S49. Gene #30: '17p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	22	28
17P MUTATED	1	16	4
17P WILD-TYPE	4	6	24

Figure S49. Get High-res Image Gene #30: '17p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_CNMF'

P value = 0.000209 (Fisher's exact test), Q value = 0.061

Table S50. Gene #30: '17p' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	11	18
17P MUTATED	19	2	2
17P WILD-TYPE	10	9	16

Figure S50. Get High-res Image Gene #30: '17p' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000326 (Fisher's exact test), Q value = 0.092

Table S51. Gene #30: '17p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	20	27
17P MUTATED	1	4	18
17P WILD-TYPE	10	16	9

Figure S51. Get High-res Image Gene #30: '17p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.0048

Table S52. Gene #30: '17p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	10	23
17P MUTATED	18	3	2
17P WILD-TYPE	7	7	21

Figure S52. Get High-res Image Gene #30: '17p' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'17p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000123 (Fisher's exact test), Q value = 0.036

Table S53. Gene #30: '17p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	26	20
17P MUTATED	1	18	4
17P WILD-TYPE	11	8	16

Figure S53. Get High-res Image Gene #30: '17p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q' versus 'CN_CNMF'

P value = 0.000309 (Fisher's exact test), Q value = 0.089

Table S54. Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	42	19
17Q MUTATED	4	2	9
17Q WILD-TYPE	16	40	10

Figure S54. Get High-res Image Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

'18q' versus 'CN_CNMF'

P value = 9.76e-05 (Fisher's exact test), Q value = 0.029

Table S55. Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	42	19
18Q MUTATED	19	17	11
18Q WILD-TYPE	1	25	8

Figure S55. Get High-res Image Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

'18q' versus 'METHLYATION_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.13

Table S56. Gene #33: '18q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	34	19
18Q MUTATED	21	11	14
18Q WILD-TYPE	6	23	5

Figure S56. Get High-res Image Gene #33: '18q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p' versus 'CN_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.2

Table S57. Gene #36: '20p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	42	19
20P MUTATED	4	5	11
20P WILD-TYPE	16	37	8

Figure S57. Get High-res Image Gene #36: '20p' versus Molecular Subtype #1: 'CN_CNMF'

'21q' versus 'CN_CNMF'

P value = 6.32e-07 (Fisher's exact test), Q value = 2e-04

Table S58. Gene #38: '21q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	42	19
21Q MUTATED	12	4	13
21Q WILD-TYPE	8	38	6

Figure S58. Get High-res Image Gene #38: '21q' versus Molecular Subtype #1: 'CN_CNMF'

'22q' versus 'CN_CNMF'

P value = 0.000177 (Fisher's exact test), Q value = 0.052

Table S59. Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	42	19
22Q MUTATED	7	3	10
22Q WILD-TYPE	13	39	9

Figure S59. Get High-res Image Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = PAAD-TP.transferedmergedcluster.txt
Number of patients = 81
Number of significantly focal cnvs = 40
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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