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
doi:10.7908/C1Z31X27
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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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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