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

Kidney Chromophobe (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/C1Z31X27

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 66 patients, 43 significant findings detected with P value < 0.05 and Q value < 0.25.

1p cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
1q cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
2p cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
2q cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4p cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
4q cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
6p cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
6q cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
8p cnv correlated to 'CN_CNMF'.
10p cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
10q cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
11q cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
13q cnv correlated to 'METHLYATION_CNMF'.
16p cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
16q cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
17p cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17q cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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, 43 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	Chi-square test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test
17p	50 (76%)	16	0.299 (1.00)	4.75e-07 (0.000152)	5.74e-07 (0.000181)	5.55e-07 (0.000177)	0.0506 (1.00)	0.000396 (0.114)	0.05 (1.00)	0.000108 (0.0323)
17q	50 (76%)	16	0.299 (1.00)	4.75e-07 (0.000152)	5.74e-07 (0.000181)	5.55e-07 (0.000177)	0.0506 (1.00)	0.000396 (0.114)	0.05 (1.00)	0.000108 (0.0323)
2p	48 (73%)	18	0.165 (1.00)	3.89e-05 (0.0119)	2.21e-06 (0.000694)	2.68e-06 (0.000836)	0.119 (1.00)	0.00103 (0.284)	0.0242 (1.00)	0.00018 (0.0531)
2q	48 (73%)	18	0.165 (1.00)	3.89e-05 (0.0119)	2.21e-06 (0.000694)	2.68e-06 (0.000836)	0.119 (1.00)	0.00103 (0.284)	0.0242 (1.00)	0.00018 (0.0531)
1p	54 (82%)	12	0.657 (1.00)	5.29e-06 (0.00164)	5.95e-05 (0.018)	1.16e-05 (0.00358)	0.315 (1.00)	0.00742 (1.00)	0.276 (1.00)	0.00427 (1.00)
1q	53 (80%)	13	0.671 (1.00)	2.22e-05 (0.00684)	0.000362 (0.105)	4.71e-05 (0.0143)	0.422 (1.00)	0.0113 (1.00)	0.201 (1.00)	0.00486 (1.00)
4p	25 (38%)	41	0.0622 (1.00)	0.779 (1.00)	7.61e-05 (0.0229)	0.000406 (0.116)	0.941 (1.00)	0.464 (1.00)	0.817 (1.00)	0.0608 (1.00)
4q	25 (38%)	41	0.0622 (1.00)	0.779 (1.00)	7.61e-05 (0.0229)	0.000406 (0.116)	0.941 (1.00)	0.464 (1.00)	0.817 (1.00)	0.0608 (1.00)
6p	52 (79%)	14	0.475 (1.00)	0.000506 (0.144)	0.000255 (0.0744)	0.0021 (0.566)	0.544 (1.00)	0.0166 (1.00)	0.319 (1.00)	0.00559 (1.00)
6q	52 (79%)	14	0.475 (1.00)	0.000506 (0.144)	0.000255 (0.0744)	0.0021 (0.566)	0.544 (1.00)	0.0166 (1.00)	0.319 (1.00)	0.00559 (1.00)
10p	52 (79%)	14	0.157 (1.00)	0.00496 (1.00)	0.000255 (0.0744)	4.55e-05 (0.0138)	0.24 (1.00)	0.0166 (1.00)	0.0525 (1.00)	0.00559 (1.00)
10q	51 (77%)	15	0.33 (1.00)	0.00128 (0.349)	0.00018 (0.0531)	3.39e-05 (0.0104)	0.355 (1.00)	0.0233 (1.00)	0.0872 (1.00)	0.00491 (1.00)
16p	25 (38%)	41	0.166 (1.00)	0.909 (1.00)	0.000589 (0.166)	0.000597 (0.167)	0.367 (1.00)	0.137 (1.00)	0.969 (1.00)	0.111 (1.00)
16q	26 (39%)	40	0.147 (1.00)	0.818 (1.00)	0.000842 (0.234)	0.00078 (0.217)	0.611 (1.00)	0.465 (1.00)	0.964 (1.00)	0.214 (1.00)
8p	26 (39%)	40	9.22e-05 (0.0276)	0.896 (1.00)	0.0434 (1.00)	0.19 (1.00)	0.918 (1.00)	0.465 (1.00)	0.399 (1.00)	0.351 (1.00)
11q	22 (33%)	44	0.677 (1.00)	0.648 (1.00)	0.00286 (0.767)	0.000592 (0.166)	0.202 (1.00)	0.253 (1.00)	0.969 (1.00)	0.0611 (1.00)
13q	45 (68%)	21	0.344 (1.00)	0.000206 (0.0603)	0.00121 (0.332)	0.0186 (1.00)	0.548 (1.00)	0.0242 (1.00)	0.998 (1.00)	0.163 (1.00)
3p	17 (26%)	49	0.362 (1.00)	0.559 (1.00)	0.507 (1.00)	0.428 (1.00)	0.896 (1.00)	1 (1.00)	0.398 (1.00)	0.421 (1.00)
3q	16 (24%)	50	0.34 (1.00)	0.217 (1.00)	0.346 (1.00)	0.278 (1.00)	1 (1.00)	1 (1.00)	0.376 (1.00)	0.362 (1.00)
5p	18 (27%)	48	0.342 (1.00)	0.118 (1.00)	0.0354 (1.00)	0.0193 (1.00)	0.549 (1.00)	0.696 (1.00)	0.455 (1.00)	0.136 (1.00)
5q	18 (27%)	48	0.342 (1.00)	0.118 (1.00)	0.0354 (1.00)	0.0193 (1.00)	0.549 (1.00)	0.696 (1.00)	0.455 (1.00)	0.136 (1.00)
7p	25 (38%)	41	0.166 (1.00)	0.909 (1.00)	0.00579 (1.00)	0.0294 (1.00)	0.652 (1.00)	1 (1.00)	0.78 (1.00)	0.314 (1.00)
7q	25 (38%)	41	0.166 (1.00)	0.909 (1.00)	0.00579 (1.00)	0.0294 (1.00)	0.652 (1.00)	1 (1.00)	0.78 (1.00)	0.314 (1.00)
8q	26 (39%)	40	0.00091 (0.252)	0.896 (1.00)	0.0194 (1.00)	0.0845 (1.00)	0.918 (1.00)	0.465 (1.00)	0.791 (1.00)	0.102 (1.00)
9p	20 (30%)	46	0.445 (1.00)	1 (1.00)	0.291 (1.00)	0.739 (1.00)	0.722 (1.00)	0.437 (1.00)	0.228 (1.00)	0.736 (1.00)
9q	20 (30%)	46	0.445 (1.00)	1 (1.00)	0.291 (1.00)	0.739 (1.00)	0.722 (1.00)	0.437 (1.00)	0.228 (1.00)	0.736 (1.00)
11p	22 (33%)	44	0.677 (1.00)	0.648 (1.00)	0.0184 (1.00)	0.00623 (1.00)	0.503 (1.00)	0.253 (1.00)	0.845 (1.00)	0.206 (1.00)
12p	21 (32%)	45	0.344 (1.00)	0.565 (1.00)	0.131 (1.00)	0.219 (1.00)	0.929 (1.00)	0.45 (1.00)	0.678 (1.00)	0.0822 (1.00)
12q	21 (32%)	45	0.409 (1.00)	0.394 (1.00)	0.167 (1.00)	0.0723 (1.00)	0.829 (1.00)	0.45 (1.00)	0.91 (1.00)	0.182 (1.00)
14q	23 (35%)	43	0.151 (1.00)	0.949 (1.00)	0.00985 (1.00)	0.0101 (1.00)	0.906 (1.00)	1 (1.00)	0.989 (1.00)	0.217 (1.00)
15q	23 (35%)	43	0.151 (1.00)	0.949 (1.00)	0.00937 (1.00)	0.0282 (1.00)	0.906 (1.00)	0.478 (1.00)	0.946 (1.00)	0.339 (1.00)
18p	25 (38%)	41	0.799 (1.00)	0.575 (1.00)	0.00476 (1.00)	0.00369 (0.974)	0.576 (1.00)	0.721 (1.00)	0.377 (1.00)	0.098 (1.00)
18q	26 (39%)	40	0.677 (1.00)	0.469 (1.00)	0.0165 (1.00)	0.00963 (1.00)	0.401 (1.00)	0.73 (1.00)	0.237 (1.00)	0.156 (1.00)
19p	20 (30%)	46	0.445 (1.00)	0.504 (1.00)	0.00939 (1.00)	0.00346 (0.919)	0.697 (1.00)	0.712 (1.00)	0.851 (1.00)	0.0993 (1.00)
19q	20 (30%)	46	0.445 (1.00)	0.504 (1.00)	0.00939 (1.00)	0.00346 (0.919)	0.697 (1.00)	0.712 (1.00)	0.851 (1.00)	0.0993 (1.00)
20p	24 (36%)	42	0.68 (1.00)	0.673 (1.00)	0.0999 (1.00)	0.0354 (1.00)	0.921 (1.00)	0.469 (1.00)	0.639 (1.00)	0.851 (1.00)
20q	24 (36%)	42	0.23 (1.00)	0.312 (1.00)	0.179 (1.00)	0.057 (1.00)	0.545 (1.00)	1 (1.00)	0.388 (1.00)	0.687 (1.00)
21q	39 (59%)	27	0.694 (1.00)	0.0787 (1.00)	0.461 (1.00)	0.215 (1.00)	1 (1.00)	1 (1.00)	0.96 (1.00)	0.373 (1.00)
22q	27 (41%)	39	0.776 (1.00)	0.677 (1.00)	0.00172 (0.466)	0.00159 (0.432)	0.81 (1.00)	0.29 (1.00)	0.912 (1.00)	0.296 (1.00)
xq	45 (68%)	21	1 (1.00)	0.188 (1.00)	0.0471 (1.00)	0.0188 (1.00)	0.0322 (1.00)	0.00337 (0.899)	0.00606 (1.00)	0.0446 (1.00)

'1p' versus 'METHLYATION_CNMF'

P value = 5.29e-06 (Fisher's exact test), Q value = 0.0016

Table S1. Gene #1: '1p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	35	13
1P MUTATED	17	33	4
1P WILD-TYPE	1	2	9

Figure S1. Get High-res Image Gene #1: '1p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p' versus 'MRNASEQ_CNMF'

P value = 5.95e-05 (Fisher's exact test), Q value = 0.018

Table S2. Gene #1: '1p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
1P MUTATED	19	16	15	4
1P WILD-TYPE	0	6	0	6

Figure S2. Get High-res Image Gene #1: '1p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.16e-05 (Chi-square test), Q value = 0.0036

Table S3. Gene #1: '1p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
1P MUTATED	10	3	12	6	23
1P WILD-TYPE	0	7	5	0	0

Figure S3. Get High-res Image Gene #1: '1p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q' versus 'METHLYATION_CNMF'

P value = 2.22e-05 (Fisher's exact test), Q value = 0.0068

Table S4. Gene #2: '1q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	35	13
1Q MUTATED	17	32	4
1Q WILD-TYPE	1	3	9

Figure S4. Get High-res Image Gene #2: '1q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q' versus 'MRNASEQ_CNMF'

P value = 0.000362 (Fisher's exact test), Q value = 0.1

Table S5. Gene #2: '1q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
1Q MUTATED	19	16	14	4
1Q WILD-TYPE	0	6	1	6

Figure S5. Get High-res Image Gene #2: '1q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.71e-05 (Chi-square test), Q value = 0.014

Table S6. Gene #2: '1q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
1Q MUTATED	10	3	12	5	23
1Q WILD-TYPE	0	7	5	1	0

Figure S6. Get High-res Image Gene #2: '1q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p' versus 'METHLYATION_CNMF'

P value = 3.89e-05 (Fisher's exact test), Q value = 0.012

Table S7. Gene #3: '2p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	35	13
2P MUTATED	17	28	3
2P WILD-TYPE	1	7	10

Figure S7. Get High-res Image Gene #3: '2p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p' versus 'MRNASEQ_CNMF'

P value = 2.21e-06 (Fisher's exact test), Q value = 0.00069

Table S8. Gene #3: '2p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
2P MUTATED	19	15	13	1
2P WILD-TYPE	0	7	2	9

Figure S8. Get High-res Image Gene #3: '2p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.68e-06 (Chi-square test), Q value = 0.00084

Table S9. Gene #3: '2p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
2P MUTATED	10	1	12	3	22
2P WILD-TYPE	0	9	5	3	1

Figure S9. Get High-res Image Gene #3: '2p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.053

Table S10. Gene #3: '2p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	8	25	21
2P MUTATED	4	5	18	21
2P WILD-TYPE	8	3	7	0

Figure S10. Get High-res Image Gene #3: '2p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q' versus 'METHLYATION_CNMF'

P value = 3.89e-05 (Fisher's exact test), Q value = 0.012

Table S11. Gene #4: '2q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	35	13
2Q MUTATED	17	28	3
2Q WILD-TYPE	1	7	10

Figure S11. Get High-res Image Gene #4: '2q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q' versus 'MRNASEQ_CNMF'

P value = 2.21e-06 (Fisher's exact test), Q value = 0.00069

Table S12. Gene #4: '2q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
2Q MUTATED	19	15	13	1
2Q WILD-TYPE	0	7	2	9

Figure S12. Get High-res Image Gene #4: '2q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.68e-06 (Chi-square test), Q value = 0.00084

Table S13. Gene #4: '2q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
2Q MUTATED	10	1	12	3	22
2Q WILD-TYPE	0	9	5	3	1

Figure S13. Get High-res Image Gene #4: '2q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.053

Table S14. Gene #4: '2q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	8	25	21
2Q MUTATED	4	5	18	21
2Q WILD-TYPE	8	3	7	0

Figure S14. Get High-res Image Gene #4: '2q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p' versus 'MRNASEQ_CNMF'

P value = 7.61e-05 (Fisher's exact test), Q value = 0.023

Table S15. Gene #7: '4p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
4P MUTATED	4	17	2	2
4P WILD-TYPE	15	5	13	8

Figure S15. Get High-res Image Gene #7: '4p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000406 (Chi-square test), Q value = 0.12

Table S16. Gene #7: '4p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
4P MUTATED	1	3	14	2	5
4P WILD-TYPE	9	7	3	4	18

Figure S16. Get High-res Image Gene #7: '4p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4q' versus 'MRNASEQ_CNMF'

P value = 7.61e-05 (Fisher's exact test), Q value = 0.023

Table S17. Gene #8: '4q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
4Q MUTATED	4	17	2	2
4Q WILD-TYPE	15	5	13	8

Figure S17. Get High-res Image Gene #8: '4q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000406 (Chi-square test), Q value = 0.12

Table S18. Gene #8: '4q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
4Q MUTATED	1	3	14	2	5
4Q WILD-TYPE	9	7	3	4	18

Figure S18. Get High-res Image Gene #8: '4q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p' versus 'METHLYATION_CNMF'

P value = 0.000506 (Fisher's exact test), Q value = 0.14

Table S19. Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	35	13
6P MUTATED	17	30	5
6P WILD-TYPE	1	5	8

Figure S19. Get High-res Image Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p' versus 'MRNASEQ_CNMF'

P value = 0.000255 (Fisher's exact test), Q value = 0.074

Table S20. Gene #11: '6p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
6P MUTATED	19	15	14	4
6P WILD-TYPE	0	7	1	6

Figure S20. Get High-res Image Gene #11: '6p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q' versus 'METHLYATION_CNMF'

P value = 0.000506 (Fisher's exact test), Q value = 0.14

Table S21. Gene #12: '6q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	35	13
6Q MUTATED	17	30	5
6Q WILD-TYPE	1	5	8

Figure S21. Get High-res Image Gene #12: '6q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q' versus 'MRNASEQ_CNMF'

P value = 0.000255 (Fisher's exact test), Q value = 0.074

Table S22. Gene #12: '6q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
6Q MUTATED	19	15	14	4
6Q WILD-TYPE	0	7	1	6

Figure S22. Get High-res Image Gene #12: '6q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p' versus 'CN_CNMF'

P value = 9.22e-05 (Fisher's exact test), Q value = 0.028

Table S23. Gene #15: '8p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	47	14
8P MUTATED	0	14	12
8P WILD-TYPE	5	33	2

Figure S23. Get High-res Image Gene #15: '8p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'MRNASEQ_CNMF'

P value = 0.000255 (Fisher's exact test), Q value = 0.074

Table S24. Gene #19: '10p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
10P MUTATED	19	15	14	4
10P WILD-TYPE	0	7	1	6

Figure S24. Get High-res Image Gene #19: '10p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.55e-05 (Chi-square test), Q value = 0.014

Table S25. Gene #19: '10p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
10P MUTATED	10	3	11	5	23
10P WILD-TYPE	0	7	6	1	0

Figure S25. Get High-res Image Gene #19: '10p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.053

Table S26. Gene #20: '10q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
10Q MUTATED	19	14	14	4
10Q WILD-TYPE	0	8	1	6

Figure S26. Get High-res Image Gene #20: '10q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.39e-05 (Chi-square test), Q value = 0.01

Table S27. Gene #20: '10q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
10Q MUTATED	10	3	10	5	23
10Q WILD-TYPE	0	7	7	1	0

Figure S27. Get High-res Image Gene #20: '10q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000592 (Chi-square test), Q value = 0.17

Table S28. Gene #22: '11q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
11Q MUTATED	1	2	13	1	5
11Q WILD-TYPE	9	8	4	5	18

Figure S28. Get High-res Image Gene #22: '11q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'13q' versus 'METHLYATION_CNMF'

P value = 0.000206 (Fisher's exact test), Q value = 0.06

Table S29. Gene #25: '13q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	35	13
13Q MUTATED	12	30	3
13Q WILD-TYPE	6	5	10

Figure S29. Get High-res Image Gene #25: '13q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p' versus 'MRNASEQ_CNMF'

P value = 0.000589 (Fisher's exact test), Q value = 0.17

Table S30. Gene #28: '16p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
16P MUTATED	4	16	4	1
16P WILD-TYPE	15	6	11	9

Figure S30. Get High-res Image Gene #28: '16p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000597 (Chi-square test), Q value = 0.17

Table S31. Gene #28: '16p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
16P MUTATED	3	2	14	1	5
16P WILD-TYPE	7	8	3	5	18

Figure S31. Get High-res Image Gene #28: '16p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q' versus 'MRNASEQ_CNMF'

P value = 0.000842 (Fisher's exact test), Q value = 0.23

Table S32. Gene #29: '16q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
16Q MUTATED	4	16	5	1
16Q WILD-TYPE	15	6	10	9

Figure S32. Get High-res Image Gene #29: '16q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00078 (Chi-square test), Q value = 0.22

Table S33. Gene #29: '16q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
16Q MUTATED	4	2	14	1	5
16Q WILD-TYPE	6	8	3	5	18

Figure S33. Get High-res Image Gene #29: '16q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p' versus 'METHLYATION_CNMF'

P value = 4.75e-07 (Fisher's exact test), Q value = 0.00015

Table S34. Gene #30: '17p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	35	13
17P MUTATED	17	31	2
17P WILD-TYPE	1	4	11

Figure S34. Get High-res Image Gene #30: '17p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p' versus 'MRNASEQ_CNMF'

P value = 5.74e-07 (Fisher's exact test), Q value = 0.00018

Table S35. Gene #30: '17p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
17P MUTATED	19	16	14	1
17P WILD-TYPE	0	6	1	9

Figure S35. Get High-res Image Gene #30: '17p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.55e-07 (Chi-square test), Q value = 0.00018

Table S36. Gene #30: '17p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
17P MUTATED	10	1	12	4	23
17P WILD-TYPE	0	9	5	2	0

Figure S36. Get High-res Image Gene #30: '17p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000396 (Fisher's exact test), Q value = 0.11

Table S37. Gene #30: '17p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	9	57
17P MUTATED	2	48
17P WILD-TYPE	7	9

Figure S37. Get High-res Image Gene #30: '17p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.032

Table S38. Gene #30: '17p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	8	25	21
17P MUTATED	4	5	20	21
17P WILD-TYPE	8	3	5	0

Figure S38. Get High-res Image Gene #30: '17p' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q' versus 'METHLYATION_CNMF'

P value = 4.75e-07 (Fisher's exact test), Q value = 0.00015

Table S39. Gene #31: '17q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	35	13
17Q MUTATED	17	31	2
17Q WILD-TYPE	1	4	11

Figure S39. Get High-res Image Gene #31: '17q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q' versus 'MRNASEQ_CNMF'

P value = 5.74e-07 (Fisher's exact test), Q value = 0.00018

Table S40. Gene #31: '17q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
17Q MUTATED	19	16	14	1
17Q WILD-TYPE	0	6	1	9

Figure S40. Get High-res Image Gene #31: '17q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.55e-07 (Chi-square test), Q value = 0.00018

Table S41. Gene #31: '17q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
17Q MUTATED	10	1	12	4	23
17Q WILD-TYPE	0	9	5	2	0

Figure S41. Get High-res Image Gene #31: '17q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000396 (Fisher's exact test), Q value = 0.11

Table S42. Gene #31: '17q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	9	57
17Q MUTATED	2	48
17Q WILD-TYPE	7	9

Figure S42. Get High-res Image Gene #31: '17q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.032

Table S43. Gene #31: '17q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	8	25	21
17Q MUTATED	4	5	20	21
17Q WILD-TYPE	8	3	5	0

Figure S43. Get High-res Image Gene #31: '17q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = KICH-TP.transferedmergedcluster.txt
Number of patients = 66
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

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

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] 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)

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