Correlation between gene mutation status and molecular subtypes
Kidney Chromophobe (Primary solid tumor)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1BR8R1B
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 gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1BR8R1B
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 4 genes and 8 molecular subtypes across 66 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.

- No gene mutations related to molecuar subtypes.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 4 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, no significant finding detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nMutated (%) | 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
TP53 | 22 (33%) | 44 | 0.615 (1.00) | 0.0891 (1.00) | 0.0657 (1.00) | 0.016 (0.495) | 0.643 (1.00) | 0.662 (1.00) | 1 (1.00) | 0.688 (1.00)
PTEN | 6 (9%) | 60 | 0.0996 (1.00) | 0.322 (1.00) | 0.352 (1.00) | 0.475 (1.00) | 0.353 (1.00) | 0.0674 (1.00) | 0.372 (1.00) | 0.374 (1.00)
PABPC1 | 7 (11%) | 59 | 0.489 (1.00) | 0.236 (1.00) | 0.204 (1.00) | 0.74 (1.00) | 0.61 (1.00) | 0.308 (1.00) | 0.286 (1.00) | 0.143 (1.00)
URGCP | 3 (5%) | 63 | 0.648 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.195 (1.00) | 0.542 (1.00) | 0.152 (1.00) |

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.615 (Fisher's exact test), Q value = 1

Table S1. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 47 | 14
TP53 MUTATED | 2 | 14 | 6
TP53 WILD-TYPE | 3 | 33 | 8

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0891 (Fisher's exact test), Q value = 1

Table S2. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
TP53 MUTATED | 3 | 16 | 3
TP53 WILD-TYPE | 15 | 19 | 10

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0657 (Fisher's exact test), Q value = 1

Table S3. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
TP53 MUTATED | 6 | 6 | 9 | 1
TP53 WILD-TYPE | 13 | 16 | 6 | 9

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.49

Table S4. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
TP53 MUTATED | 5 | 6 | 1 | 0 | 7 | 3 | 0
TP53 WILD-TYPE | 14 | 10 | 6 | 6 | 3 | 1 | 4

Figure S1. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.643 (Fisher's exact test), Q value = 1

Table S5. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 24 | 22
TP53 MUTATED | 5 | 9 | 8
TP53 WILD-TYPE | 15 | 15 | 14

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.662 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
TP53 MUTATED | 7 | 5 | 3 | 1 | 1 | 3 | 2
TP53 WILD-TYPE | 11 | 6 | 9 | 5 | 4 | 2 | 7

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S7. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 29
TP53 MUTATED | 7 | 11
TP53 WILD-TYPE | 12 | 18

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.688 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 10 | 6 | 5 | 8 | 4 | 6 | 5 | 4
TP53 MUTATED | 4 | 3 | 2 | 2 | 1 | 3 | 3 | 0
TP53 WILD-TYPE | 6 | 3 | 3 | 6 | 3 | 3 | 2 | 4

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0996 (Fisher's exact test), Q value = 1

Table S9. Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 47 | 14
PTEN MUTATED | 2 | 3 | 1
PTEN WILD-TYPE | 3 | 44 | 13

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 1

Table S10. Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
PTEN MUTATED | 3 | 3 | 0
PTEN WILD-TYPE | 15 | 32 | 13

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.352 (Fisher's exact test), Q value = 1

Table S11. Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
PTEN MUTATED | 2 | 1 | 3 | 0
PTEN WILD-TYPE | 17 | 21 | 12 | 10

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.475 (Fisher's exact test), Q value = 1

Table S12. Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
PTEN MUTATED | 2 | 1 | 0 | 0 | 3 | 0 | 0
PTEN WILD-TYPE | 17 | 15 | 7 | 6 | 7 | 4 | 4

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 24 | 22
PTEN MUTATED | 1 | 4 | 1
PTEN WILD-TYPE | 19 | 20 | 21

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0674 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
PTEN MUTATED | 5 | 0 | 0 | 0 | 0 | 1 | 0
PTEN WILD-TYPE | 13 | 11 | 12 | 6 | 5 | 4 | 9

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 1

Table S15. Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 29
PTEN MUTATED | 3 | 2
PTEN WILD-TYPE | 16 | 27

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 1

Table S16. Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 10 | 6 | 5 | 8 | 4 | 6 | 5 | 4
PTEN MUTATED | 3 | 0 | 1 | 0 | 0 | 0 | 1 | 0
PTEN WILD-TYPE | 7 | 6 | 4 | 8 | 4 | 6 | 4 | 4

'PABPC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 1

Table S17. Gene #3: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 47 | 14
PABPC1 MUTATED | 1 | 4 | 2
PABPC1 WILD-TYPE | 4 | 43 | 12

'PABPC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 1

Table S18. Gene #3: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
PABPC1 MUTATED | 2 | 2 | 3
PABPC1 WILD-TYPE | 16 | 33 | 10

'PABPC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.204 (Fisher's exact test), Q value = 1

Table S19. Gene #3: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
PABPC1 MUTATED | 2 | 1 | 1 | 3
PABPC1 WILD-TYPE | 17 | 21 | 14 | 7

'PABPC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S20. Gene #3: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
PABPC1 MUTATED | 2 | 1 | 2 | 1 | 1 | 0 | 0
PABPC1 WILD-TYPE | 17 | 15 | 5 | 5 | 9 | 4 | 4

'PABPC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.61 (Fisher's exact test), Q value = 1

Table S21. Gene #3: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 24 | 22
PABPC1 MUTATED | 3 | 3 | 1
PABPC1 WILD-TYPE | 17 | 21 | 21

'PABPC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.308 (Fisher's exact test), Q value = 1

Table S22. Gene #3: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
PABPC1 MUTATED | 2 | 1 | 0 | 1 | 0 | 0 | 3
PABPC1 WILD-TYPE | 16 | 10 | 12 | 5 | 5 | 5 | 6

'PABPC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.286 (Fisher's exact test), Q value = 1

Table S23. Gene #3: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 29
PABPC1 MUTATED | 3 | 1
PABPC1 WILD-TYPE | 16 | 28

'PABPC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.143 (Fisher's exact test), Q value = 1

Table S24. Gene #3: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 10 | 6 | 5 | 8 | 4 | 6 | 5 | 4
PABPC1 MUTATED | 0 | 0 | 1 | 0 | 0 | 2 | 1 | 0
PABPC1 WILD-TYPE | 10 | 6 | 4 | 8 | 4 | 4 | 4 | 4

'URGCP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S25. Gene #4: 'URGCP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 47 | 14
URGCP MUTATED | 0 | 2 | 1
URGCP WILD-TYPE | 5 | 45 | 13

'URGCP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S26. Gene #4: 'URGCP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
URGCP MUTATED | 1 | 2 | 0
URGCP WILD-TYPE | 17 | 33 | 13

'URGCP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S27. Gene #4: 'URGCP MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
URGCP MUTATED | 1 | 1 | 1 | 0
URGCP WILD-TYPE | 18 | 21 | 14 | 10

'URGCP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S28. Gene #4: 'URGCP MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4
URGCP MUTATED | 1 | 1 | 0 | 0 | 1 | 0 | 0
URGCP WILD-TYPE | 18 | 15 | 7 | 6 | 9 | 4 | 4

'URGCP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.195 (Fisher's exact test), Q value = 1

Table S29. Gene #4: 'URGCP MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 24 | 22
URGCP MUTATED | 2 | 0 | 1
URGCP WILD-TYPE | 18 | 24 | 21

'URGCP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.542 (Fisher's exact test), Q value = 1

Table S30. Gene #4: 'URGCP MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9
URGCP MUTATED | 1 | 0 | 0 | 1 | 0 | 0 | 1
URGCP WILD-TYPE | 17 | 11 | 12 | 5 | 5 | 5 | 8

'URGCP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 1

Table S31. Gene #4: 'URGCP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 19 | 29
URGCP MUTATED | 2 | 0
URGCP WILD-TYPE | 17 | 29

Methods & Data
Input

- Mutation data file = transformed.cor.cli.txt

- Molecular subtypes file = KICH-TP.transferedmergedcluster.txt

- Number of patients = 66

- Number of significantly mutated genes = 4

- Number of Molecular subtypes = 8

- Exclude genes that fewer than K tumors have mutations, 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.

- 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] 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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