Correlation between gene mutation status and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1V40SVX
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/C1V40SVX
Overview
Introduction

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

Summary

Testing the association between mutation status of 7 genes and 8 molecular subtypes across 168 patients, 4 significant findings detected with P value < 0.05 and Q value < 0.25.

- NEFH mutation correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- ZNF598 mutation correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 7 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, 4 significant findings detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nMutated (%) | nWild-Type | Chi-square test | Chi-square 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
NEFH | 10 (6%) | 158 | 0.423 (1.00) | 0.567 (1.00) | 0.0614 (1.00) | 0.426 (1.00) | 0.0235 (1.00) | 0.00043 (0.0232) | 0.0157 (0.802) | 0.003 (0.159)
ZNF598 | 13 (8%) | 155 | 0.134 (1.00) | 0.379 (1.00) | 0.0978 (1.00) | 0.385 (1.00) | 0.675 (1.00) | 0.0004 (0.022) | 0.452 (1.00) | 0.000209 (0.0117)
SKI | 6 (4%) | 162 | 0.0954 (1.00) | 0.0833 (1.00) | 0.127 (1.00) | 0.674 (1.00) | 0.696 (1.00) | 0.38 (1.00) | 0.776 (1.00) | 0.858 (1.00)
HNRNPM | 11 (7%) | 157 | 0.309 (1.00) | 0.845 (1.00) | 0.828 (1.00) | 0.258 (1.00) | 0.544 (1.00) | 0.345 (1.00) | 0.682 (1.00) | 0.403 (1.00)
NF2 | 12 (7%) | 156 | 0.0523 (1.00) | 0.0338 (1.00) | 0.0768 (1.00) | 0.932 (1.00) | 0.93 (1.00) | 0.609 (1.00) | 0.868 (1.00) | 1 (1.00)
BMS1 | 13 (8%) | 155 | 0.906 (1.00) | 0.52 (1.00) | 0.324 (1.00) | 0.876 (1.00) | 0.59 (1.00) | 0.0991 (1.00) | 1 (1.00) | 0.323 (1.00)
MUC2 | 26 (15%) | 142 | 0.164 (1.00) | 0.319 (1.00) | 0.00856 (0.445) | 0.0821 (1.00) | 0.712 (1.00) | 0.171 (1.00) | 0.34 (1.00) | 0.317 (1.00)

'SKI MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0954 (Chi-square test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 59 | 34 | 37 | 16 | 22
SKI MUTATED | 5 | 0 | 0 | 1 | 0
SKI WILD-TYPE | 54 | 34 | 37 | 15 | 22

'SKI MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0833 (Chi-square test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 33 | 23 | 30 | 38 | 29
SKI MUTATED | 4 | 0 | 0 | 1 | 1
SKI WILD-TYPE | 29 | 23 | 30 | 37 | 28

'SKI MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 32 | 64 | 47 | 25
SKI MUTATED | 1 | 1 | 1 | 3
SKI WILD-TYPE | 31 | 63 | 46 | 22

'SKI MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.674 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 63 | 48
SKI MUTATED | 1 | 3 | 2
SKI WILD-TYPE | 56 | 60 | 46

'SKI MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.696 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 55 | 58 | 55
SKI MUTATED | 3 | 2 | 1
SKI WILD-TYPE | 52 | 56 | 54

'SKI MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 70 | 73
SKI MUTATED | 2 | 2 | 2
SKI WILD-TYPE | 23 | 68 | 71

'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.776 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 52 | 61 | 55
SKI MUTATED | 2 | 3 | 1
SKI WILD-TYPE | 50 | 58 | 54

'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.858 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 66 | 82 | 20
SKI MUTATED | 2 | 3 | 1
SKI WILD-TYPE | 64 | 79 | 19

'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.423 (Chi-square test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 59 | 34 | 37 | 16 | 22
NEFH MUTATED | 2 | 1 | 3 | 1 | 3
NEFH WILD-TYPE | 57 | 33 | 34 | 15 | 19

'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.567 (Chi-square test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 33 | 23 | 30 | 38 | 29
NEFH MUTATED | 2 | 0 | 3 | 3 | 1
NEFH WILD-TYPE | 31 | 23 | 27 | 35 | 28

'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0614 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 32 | 64 | 47 | 25
NEFH MUTATED | 5 | 2 | 3 | 0
NEFH WILD-TYPE | 27 | 62 | 44 | 25

'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.426 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 63 | 48
NEFH MUTATED | 4 | 5 | 1
NEFH WILD-TYPE | 53 | 58 | 47

'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 55 | 58 | 55
NEFH MUTATED | 6 | 0 | 4
NEFH WILD-TYPE | 49 | 58 | 51

Figure S1. Get High-res Image Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.023

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 70 | 73
NEFH MUTATED | 0 | 0 | 10
NEFH WILD-TYPE | 25 | 70 | 63

Figure S2. Get High-res Image Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.8

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 52 | 61 | 55
NEFH MUTATED | 4 | 0 | 6
NEFH WILD-TYPE | 48 | 61 | 49

Figure S3. Get High-res Image Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.003 (Fisher's exact test), Q value = 0.16

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 66 | 82 | 20
NEFH MUTATED | 0 | 10 | 0
NEFH WILD-TYPE | 66 | 72 | 20

Figure S4. Get High-res Image Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HNRNPM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.309 (Chi-square test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 59 | 34 | 37 | 16 | 22
HNRNPM MUTATED | 6 | 0 | 2 | 2 | 1
HNRNPM WILD-TYPE | 53 | 34 | 35 | 14 | 21

'HNRNPM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.845 (Chi-square test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 33 | 23 | 30 | 38 | 29
HNRNPM MUTATED | 2 | 2 | 2 | 4 | 1
HNRNPM WILD-TYPE | 31 | 21 | 28 | 34 | 28

'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.828 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 32 | 64 | 47 | 25
HNRNPM MUTATED | 1 | 4 | 4 | 2
HNRNPM WILD-TYPE | 31 | 60 | 43 | 23

'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.258 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 63 | 48
HNRNPM MUTATED | 6 | 2 | 3
HNRNPM WILD-TYPE | 51 | 61 | 45

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 55 | 58 | 55
HNRNPM MUTATED | 2 | 4 | 5
HNRNPM WILD-TYPE | 53 | 54 | 50

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.345 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 70 | 73
HNRNPM MUTATED | 1 | 7 | 3
HNRNPM WILD-TYPE | 24 | 63 | 70

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.682 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 52 | 61 | 55
HNRNPM MUTATED | 2 | 5 | 4
HNRNPM WILD-TYPE | 50 | 56 | 51

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.403 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 66 | 82 | 20
HNRNPM MUTATED | 6 | 5 | 0
HNRNPM WILD-TYPE | 60 | 77 | 20

'NF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0523 (Chi-square test), Q value = 1

Table S25. Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 59 | 34 | 37 | 16 | 22
NF2 MUTATED | 2 | 1 | 6 | 0 | 3
NF2 WILD-TYPE | 57 | 33 | 31 | 16 | 19

'NF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0338 (Chi-square test), Q value = 1

Table S26. Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 33 | 23 | 30 | 38 | 29
NF2 MUTATED | 0 | 4 | 2 | 5 | 0
NF2 WILD-TYPE | 33 | 19 | 28 | 33 | 29

Figure S5. Get High-res Image Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0768 (Fisher's exact test), Q value = 1

Table S27. Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 32 | 64 | 47 | 25
NF2 MUTATED | 0 | 7 | 5 | 0
NF2 WILD-TYPE | 32 | 57 | 42 | 25

'NF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.932 (Fisher's exact test), Q value = 1

Table S28. Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 63 | 48
NF2 MUTATED | 4 | 4 | 4
NF2 WILD-TYPE | 53 | 59 | 44

'NF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S29. Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 55 | 58 | 55
NF2 MUTATED | 4 | 5 | 3
NF2 WILD-TYPE | 51 | 53 | 52

'NF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.609 (Fisher's exact test), Q value = 1

Table S30. Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 70 | 73
NF2 MUTATED | 1 | 4 | 7
NF2 WILD-TYPE | 24 | 66 | 66

'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S31. Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 52 | 61 | 55
NF2 MUTATED | 4 | 5 | 3
NF2 WILD-TYPE | 48 | 56 | 52

'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S32. Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 66 | 82 | 20
NF2 MUTATED | 5 | 6 | 1
NF2 WILD-TYPE | 61 | 76 | 19

'ZNF598 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.134 (Chi-square test), Q value = 1

Table S33. Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 59 | 34 | 37 | 16 | 22
ZNF598 MUTATED | 5 | 0 | 5 | 0 | 3
ZNF598 WILD-TYPE | 54 | 34 | 32 | 16 | 19

'ZNF598 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.379 (Chi-square test), Q value = 1

Table S34. Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 33 | 23 | 30 | 38 | 29
ZNF598 MUTATED | 3 | 4 | 1 | 2 | 2
ZNF598 WILD-TYPE | 30 | 19 | 29 | 36 | 27

'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0978 (Fisher's exact test), Q value = 1

Table S35. Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 32 | 64 | 47 | 25
ZNF598 MUTATED | 1 | 5 | 2 | 5
ZNF598 WILD-TYPE | 31 | 59 | 45 | 20

'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S36. Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 63 | 48
ZNF598 MUTATED | 3 | 4 | 6
ZNF598 WILD-TYPE | 54 | 59 | 42

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 1

Table S37. Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 55 | 58 | 55
ZNF598 MUTATED | 3 | 6 | 4
ZNF598 WILD-TYPE | 52 | 52 | 51

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.022

Table S38. Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 70 | 73
ZNF598 MUTATED | 5 | 8 | 0
ZNF598 WILD-TYPE | 20 | 62 | 73

Figure S6. Get High-res Image Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 1

Table S39. Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 52 | 61 | 55
ZNF598 MUTATED | 3 | 7 | 3
ZNF598 WILD-TYPE | 49 | 54 | 52

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000209 (Fisher's exact test), Q value = 0.012

Table S40. Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 66 | 82 | 20
ZNF598 MUTATED | 10 | 0 | 3
ZNF598 WILD-TYPE | 56 | 82 | 17

Figure S7. Get High-res Image Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'BMS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.906 (Chi-square test), Q value = 1

Table S41. Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 59 | 34 | 37 | 16 | 22
BMS1 MUTATED | 6 | 2 | 3 | 1 | 1
BMS1 WILD-TYPE | 53 | 32 | 34 | 15 | 21

'BMS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.52 (Chi-square test), Q value = 1

Table S42. Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 33 | 23 | 30 | 38 | 29
BMS1 MUTATED | 3 | 1 | 1 | 2 | 4
BMS1 WILD-TYPE | 30 | 22 | 29 | 36 | 25

'BMS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S43. Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 32 | 64 | 47 | 25
BMS1 MUTATED | 3 | 3 | 3 | 4
BMS1 WILD-TYPE | 29 | 61 | 44 | 21

'BMS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S44. Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 63 | 48
BMS1 MUTATED | 5 | 4 | 4
BMS1 WILD-TYPE | 52 | 59 | 44

'BMS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 1

Table S45. Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 55 | 58 | 55
BMS1 MUTATED | 6 | 4 | 3
BMS1 WILD-TYPE | 49 | 54 | 52

'BMS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0991 (Fisher's exact test), Q value = 1

Table S46. Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 70 | 73
BMS1 MUTATED | 3 | 2 | 8
BMS1 WILD-TYPE | 22 | 68 | 65

'BMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S47. Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 52 | 61 | 55
BMS1 MUTATED | 4 | 5 | 4
BMS1 WILD-TYPE | 48 | 56 | 51

'BMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.323 (Fisher's exact test), Q value = 1

Table S48. Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 66 | 82 | 20
BMS1 MUTATED | 3 | 9 | 1
BMS1 WILD-TYPE | 63 | 73 | 19

'MUC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.164 (Chi-square test), Q value = 1

Table S49. Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 59 | 34 | 37 | 16 | 22
MUC2 MUTATED | 8 | 2 | 10 | 3 | 3
MUC2 WILD-TYPE | 51 | 32 | 27 | 13 | 19

'MUC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.319 (Chi-square test), Q value = 1

Table S50. Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 33 | 23 | 30 | 38 | 29
MUC2 MUTATED | 7 | 5 | 5 | 6 | 1
MUC2 WILD-TYPE | 26 | 18 | 25 | 32 | 28

'MUC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00856 (Fisher's exact test), Q value = 0.45

Table S51. Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 32 | 64 | 47 | 25
MUC2 MUTATED | 11 | 10 | 4 | 1
MUC2 WILD-TYPE | 21 | 54 | 43 | 24

Figure S8. Get High-res Image Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'MUC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0821 (Fisher's exact test), Q value = 1

Table S52. Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 63 | 48
MUC2 MUTATED | 6 | 15 | 5
MUC2 WILD-TYPE | 51 | 48 | 43

'MUC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.712 (Fisher's exact test), Q value = 1

Table S53. Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 55 | 58 | 55
MUC2 MUTATED | 10 | 9 | 7
MUC2 WILD-TYPE | 45 | 49 | 48

'MUC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.171 (Fisher's exact test), Q value = 1

Table S54. Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 70 | 73
MUC2 MUTATED | 6 | 7 | 13
MUC2 WILD-TYPE | 19 | 63 | 60

'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 1

Table S55. Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 52 | 61 | 55
MUC2 MUTATED | 11 | 9 | 6
MUC2 WILD-TYPE | 41 | 52 | 49

'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 1

Table S56. Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 66 | 82 | 20
MUC2 MUTATED | 7 | 15 | 4
MUC2 WILD-TYPE | 59 | 67 | 16

Methods & Data
Input

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

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

- Number of patients = 168

- Number of significantly mutated genes = 7

- Number of Molecular subtypes = 8

- Exclude genes that fewer than K tumors have mutations, K = 3

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

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[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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