Correlation between gene mutation status and molecular subtypes
Kidney Chromophobe (Primary solid tumor)
15 January 2014 | analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C12R3Q5B
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/C12R3Q5B
Overview
Introduction

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

Summary

Testing the association between mutation status of 6 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 6 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 | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test
MUC2 | 8 (12%) | 58 | 1 (1.00) | 0.276 (1.00) | 0.745 (1.00) | 0.71 (1.00) | 0.572 (1.00) | 0.586 (1.00) | 0.49 (1.00) | 0.481 (1.00)
MUC6 | 21 (32%) | 45 | 0.178 (1.00) | 0.634 (1.00) | 0.253 (1.00) | 0.174 (1.00) | 0.306 (1.00) | 0.252 (1.00) | 0.205 (1.00) | 0.267 (1.00)
TP53 | 22 (33%) | 44 | 0.615 (1.00) | 0.0856 (1.00) | 0.0665 (1.00) | 0.0593 (1.00) | 0.655 (1.00) | 0.706 (1.00) | 0.76 (1.00) | 0.86 (1.00)
PTEN | 6 (9%) | 60 | 0.0988 (1.00) | 0.321 (1.00) | 0.351 (1.00) | 0.13 (1.00) | 0.354 (1.00) | 0.585 (1.00) | 0.00617 (0.296) | 0.0812 (1.00)
PRSS3 | 7 (11%) | 59 | 0.386 (1.00) | 0.668 (1.00) | 0.0182 (0.855) | 0.252 (1.00) | 0.0815 (1.00) | 0.581 (1.00) | 0.61 (1.00) | 0.159 (1.00)
HLA-C | 7 (11%) | 59 | 0.49 (1.00) | 0.574 (1.00) | 0.714 (1.00) | 0.569 (1.00) | 0.158 (1.00) | 0.581 (1.00) | 0.401 (1.00) | 0.561 (1.00)

'MUC2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S1. Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 47 | 14
MUC2 MUTATED | 0 | 6 | 2
MUC2 WILD-TYPE | 5 | 41 | 12

'MUC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.276 (Fisher's exact test), Q value = 1

Table S2. Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
MUC2 MUTATED | 2 | 6 | 0
MUC2 WILD-TYPE | 16 | 29 | 13

'MUC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.745 (Fisher's exact test), Q value = 1

Table S3. Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
MUC2 MUTATED | 3 | 3 | 2 | 0
MUC2 WILD-TYPE | 16 | 19 | 13 | 10

'MUC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.71 (Chi-square test), Q value = 1

Table S4. Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
MUC2 MUTATED | 1 | 0 | 2 | 1 | 4
MUC2 WILD-TYPE | 9 | 10 | 15 | 5 | 19

'MUC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.572 (Fisher's exact test), Q value = 1

Table S5. Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 24 | 22
MUC2 MUTATED | 1 | 4 | 3
MUC2 WILD-TYPE | 19 | 20 | 19

'MUC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.586 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 9 | 57
MUC2 MUTATED | 0 | 8
MUC2 WILD-TYPE | 9 | 49

'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.49 (Chi-square test), Q value = 1

Table S7. Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 16 | 16 | 10 | 14
MUC2 MUTATED | 1 | 1 | 4 | 1 | 1
MUC2 WILD-TYPE | 9 | 15 | 12 | 9 | 13

'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
MUC2 MUTATED | 0 | 1 | 3 | 4
MUC2 WILD-TYPE | 12 | 7 | 22 | 17

'MUC6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 1

Table S9. Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 47 | 14
MUC6 MUTATED | 2 | 12 | 7
MUC6 WILD-TYPE | 3 | 35 | 7

'MUC6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S10. Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
MUC6 MUTATED | 7 | 11 | 3
MUC6 WILD-TYPE | 11 | 24 | 10

'MUC6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.253 (Fisher's exact test), Q value = 1

Table S11. Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
MUC6 MUTATED | 6 | 10 | 4 | 1
MUC6 WILD-TYPE | 13 | 12 | 11 | 9

'MUC6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.174 (Chi-square test), Q value = 1

Table S12. Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
MUC6 MUTATED | 2 | 1 | 9 | 2 | 7
MUC6 WILD-TYPE | 8 | 9 | 8 | 4 | 16

'MUC6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 24 | 22
MUC6 MUTATED | 4 | 10 | 7
MUC6 WILD-TYPE | 16 | 14 | 15

'MUC6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.252 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 9 | 57
MUC6 MUTATED | 1 | 20
MUC6 WILD-TYPE | 8 | 37

'MUC6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.205 (Chi-square test), Q value = 1

Table S15. Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 16 | 16 | 10 | 14
MUC6 MUTATED | 6 | 5 | 3 | 4 | 3
MUC6 WILD-TYPE | 4 | 11 | 13 | 6 | 11

'MUC6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.267 (Fisher's exact test), Q value = 1

Table S16. Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
MUC6 MUTATED | 1 | 3 | 9 | 8
MUC6 WILD-TYPE | 11 | 5 | 16 | 13

'TP53 MUTATION STATUS' versus 'CN_CNMF'

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

Table S17. Gene #3: '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 = 0.0856 (Fisher's exact test), Q value = 1

Table S18. Gene #3: '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 = 0.0665 (Fisher's exact test), Q value = 1

Table S19. Gene #3: '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 = 0.0593 (Chi-square test), Q value = 1

Table S20. Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
TP53 MUTATED | 7 | 1 | 6 | 2 | 6
TP53 WILD-TYPE | 3 | 9 | 11 | 4 | 17

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.655 (Fisher's exact test), Q value = 1

Table S21. Gene #3: '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 = 0.706 (Fisher's exact test), Q value = 1

Table S22. Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 9 | 57
TP53 MUTATED | 2 | 20
TP53 WILD-TYPE | 7 | 37

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.76 (Chi-square test), Q value = 1

Table S23. Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 16 | 16 | 10 | 14
TP53 MUTATED | 5 | 5 | 4 | 3 | 5
TP53 WILD-TYPE | 5 | 11 | 12 | 7 | 9

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S24. Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
TP53 MUTATED | 3 | 3 | 8 | 8
TP53 WILD-TYPE | 9 | 5 | 17 | 13

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0988 (Fisher's exact test), Q value = 1

Table S25. Gene #4: '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 = 0.321 (Fisher's exact test), Q value = 1

Table S26. Gene #4: '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 = 0.351 (Fisher's exact test), Q value = 1

Table S27. Gene #4: '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 = 0.13 (Chi-square test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
PTEN MUTATED | 3 | 0 | 1 | 0 | 2
PTEN WILD-TYPE | 7 | 10 | 16 | 6 | 21

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 1

Table S29. Gene #4: '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 = 0.585 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 9 | 57
PTEN MUTATED | 0 | 6
PTEN WILD-TYPE | 9 | 51

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00617 (Chi-square test), Q value = 0.3

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 16 | 16 | 10 | 14
PTEN MUTATED | 4 | 0 | 1 | 0 | 1
PTEN WILD-TYPE | 6 | 16 | 15 | 10 | 13

Figure S1. Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0812 (Fisher's exact test), Q value = 1

Table S32. Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
PTEN MUTATED | 0 | 0 | 1 | 5
PTEN WILD-TYPE | 12 | 8 | 24 | 16

'PRSS3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.386 (Fisher's exact test), Q value = 1

Table S33. Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 5 | 47 | 14
PRSS3 MUTATED | 0 | 4 | 3
PRSS3 WILD-TYPE | 5 | 43 | 11

'PRSS3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.668 (Fisher's exact test), Q value = 1

Table S34. Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
PRSS3 MUTATED | 1 | 4 | 2
PRSS3 WILD-TYPE | 17 | 31 | 11

'PRSS3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.86

Table S35. Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
PRSS3 MUTATED | 0 | 6 | 1 | 0
PRSS3 WILD-TYPE | 19 | 16 | 14 | 10

Figure S2. Get High-res Image Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PRSS3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.252 (Chi-square test), Q value = 1

Table S36. Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
PRSS3 MUTATED | 1 | 0 | 4 | 1 | 1
PRSS3 WILD-TYPE | 9 | 10 | 13 | 5 | 22

'PRSS3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0815 (Fisher's exact test), Q value = 1

Table S37. Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 24 | 22
PRSS3 MUTATED | 3 | 0 | 4
PRSS3 WILD-TYPE | 17 | 24 | 18

'PRSS3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.581 (Fisher's exact test), Q value = 1

Table S38. Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 9 | 57
PRSS3 MUTATED | 0 | 7
PRSS3 WILD-TYPE | 9 | 50

'PRSS3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.61 (Chi-square test), Q value = 1

Table S39. Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 16 | 16 | 10 | 14
PRSS3 MUTATED | 0 | 2 | 1 | 2 | 2
PRSS3 WILD-TYPE | 10 | 14 | 15 | 8 | 12

'PRSS3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.159 (Fisher's exact test), Q value = 1

Table S40. Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
PRSS3 MUTATED | 2 | 1 | 4 | 0
PRSS3 WILD-TYPE | 10 | 7 | 21 | 21

'HLA-C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 1

Table S41. Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

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

'HLA-C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.574 (Fisher's exact test), Q value = 1

Table S42. Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 35 | 13
HLA-C MUTATED | 3 | 3 | 1
HLA-C WILD-TYPE | 15 | 32 | 12

'HLA-C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S43. Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 19 | 22 | 15 | 10
HLA-C MUTATED | 3 | 3 | 1 | 0
HLA-C WILD-TYPE | 16 | 19 | 14 | 10

'HLA-C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.569 (Chi-square test), Q value = 1

Table S44. Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 10 | 17 | 6 | 23
HLA-C MUTATED | 1 | 0 | 3 | 0 | 3
HLA-C WILD-TYPE | 9 | 10 | 14 | 6 | 20

'HLA-C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 1

Table S45. Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 20 | 24 | 22
HLA-C MUTATED | 0 | 3 | 4
HLA-C WILD-TYPE | 20 | 21 | 18

'HLA-C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.581 (Fisher's exact test), Q value = 1

Table S46. Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 9 | 57
HLA-C MUTATED | 0 | 7
HLA-C WILD-TYPE | 9 | 50

'HLA-C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.401 (Chi-square test), Q value = 1

Table S47. Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 10 | 16 | 16 | 10 | 14
HLA-C MUTATED | 1 | 1 | 3 | 2 | 0
HLA-C WILD-TYPE | 9 | 15 | 13 | 8 | 14

'HLA-C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.561 (Fisher's exact test), Q value = 1

Table S48. Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 12 | 8 | 25 | 21
HLA-C MUTATED | 0 | 1 | 4 | 2
HLA-C WILD-TYPE | 12 | 7 | 21 | 19

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 = 6

- 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

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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