This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 4 genes and 8 molecular subtypes across 39 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
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No gene mutations related to molecuar subtypes.
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 | 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 | |
PIK3CA | 9 (23%) | 30 |
0.0309 (0.927) |
0.461 (1.00) |
0.422 (1.00) |
0.687 (1.00) |
0.677 (1.00) |
0.431 (1.00) |
1 (1.00) |
0.627 (1.00) |
TMCC1 | 4 (10%) | 35 |
0.397 (1.00) |
0.736 (1.00) |
1 (1.00) |
1 (1.00) |
0.8 (1.00) |
0.589 (1.00) |
0.257 (1.00) |
|
UGT3A2 | 3 (8%) | 36 |
0.881 (1.00) |
0.118 (1.00) |
0.343 (1.00) |
1 (1.00) |
0.52 (1.00) |
1 (1.00) |
0.42 (1.00) |
|
MAPK1 | 3 (8%) | 36 |
0.0426 (1.00) |
0.647 (1.00) |
0.667 (1.00) |
1 (1.00) |
0.407 (1.00) |
1 (1.00) |
1 (1.00) |
0.672 (1.00) |
P value = 0.0309 (Fisher's exact test), Q value = 0.93
Table S1. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 15 | 9 | 12 |
PIK3CA MUTATED | 3 | 0 | 6 |
PIK3CA WILD-TYPE | 12 | 9 | 6 |
Figure S1. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.461 (Chi-square test), Q value = 1
Table S2. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 6 | 7 | 7 | 5 | 1 | 2 |
PIK3CA MUTATED | 4 | 0 | 3 | 1 | 1 | 0 | 0 |
PIK3CA WILD-TYPE | 7 | 6 | 4 | 6 | 4 | 1 | 2 |
P value = 0.422 (Chi-square test), Q value = 1
Table S3. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 15 | 5 | 5 | 7 | 6 |
PIK3CA MUTATED | 5 | 1 | 2 | 0 | 1 |
PIK3CA WILD-TYPE | 10 | 4 | 3 | 7 | 5 |
P value = 0.687 (Fisher's exact test), Q value = 1
Table S4. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 6 | 4 | 28 |
PIK3CA MUTATED | 1 | 0 | 8 |
PIK3CA WILD-TYPE | 5 | 4 | 20 |
P value = 0.677 (Fisher's exact test), Q value = 1
Table S5. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 21 | 6 | 12 |
PIK3CA MUTATED | 4 | 2 | 3 |
PIK3CA WILD-TYPE | 17 | 4 | 9 |
P value = 0.431 (Fisher's exact test), Q value = 1
Table S6. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 8 | 6 | 6 |
PIK3CA MUTATED | 6 | 1 | 2 | 0 |
PIK3CA WILD-TYPE | 13 | 7 | 4 | 6 |
P value = 1 (Fisher's exact test), Q value = 1
Table S7. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 6 | 7 |
PIK3CA MUTATED | 6 | 1 | 2 |
PIK3CA WILD-TYPE | 20 | 5 | 5 |
P value = 0.627 (Fisher's exact test), Q value = 1
Table S8. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 4 | 25 | 10 |
PIK3CA MUTATED | 0 | 6 | 3 |
PIK3CA WILD-TYPE | 4 | 19 | 7 |
P value = 0.397 (Chi-square test), Q value = 1
Table S9. Gene #2: 'TMCC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 6 | 7 | 7 | 5 | 1 | 2 |
TMCC1 MUTATED | 3 | 1 | 0 | 0 | 0 | 0 | 0 |
TMCC1 WILD-TYPE | 8 | 5 | 7 | 7 | 5 | 1 | 2 |
P value = 0.736 (Chi-square test), Q value = 1
Table S10. Gene #2: 'TMCC1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 15 | 5 | 5 | 7 | 6 |
TMCC1 MUTATED | 2 | 0 | 1 | 1 | 0 |
TMCC1 WILD-TYPE | 13 | 5 | 4 | 6 | 6 |
P value = 1 (Fisher's exact test), Q value = 1
Table S11. Gene #2: 'TMCC1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 6 | 4 | 28 |
TMCC1 MUTATED | 0 | 0 | 4 |
TMCC1 WILD-TYPE | 6 | 4 | 24 |
P value = 1 (Fisher's exact test), Q value = 1
Table S12. Gene #2: 'TMCC1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 21 | 6 | 12 |
TMCC1 MUTATED | 3 | 0 | 1 |
TMCC1 WILD-TYPE | 18 | 6 | 11 |
P value = 0.8 (Fisher's exact test), Q value = 1
Table S13. Gene #2: 'TMCC1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 8 | 6 | 6 |
TMCC1 MUTATED | 3 | 1 | 0 | 0 |
TMCC1 WILD-TYPE | 16 | 7 | 6 | 6 |
P value = 0.589 (Fisher's exact test), Q value = 1
Table S14. Gene #2: 'TMCC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 6 | 7 |
TMCC1 MUTATED | 4 | 0 | 0 |
TMCC1 WILD-TYPE | 22 | 6 | 7 |
P value = 0.257 (Fisher's exact test), Q value = 1
Table S15. Gene #2: 'TMCC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 4 | 25 | 10 |
TMCC1 MUTATED | 1 | 3 | 0 |
TMCC1 WILD-TYPE | 3 | 22 | 10 |
P value = 0.881 (Chi-square test), Q value = 1
Table S16. Gene #3: 'UGT3A2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 6 | 7 | 7 | 5 | 1 | 2 |
UGT3A2 MUTATED | 1 | 1 | 0 | 1 | 0 | 0 | 0 |
UGT3A2 WILD-TYPE | 10 | 5 | 7 | 6 | 5 | 1 | 2 |
P value = 0.118 (Chi-square test), Q value = 1
Table S17. Gene #3: 'UGT3A2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 15 | 5 | 5 | 7 | 6 |
UGT3A2 MUTATED | 0 | 0 | 1 | 2 | 0 |
UGT3A2 WILD-TYPE | 15 | 5 | 4 | 5 | 6 |
P value = 0.343 (Fisher's exact test), Q value = 1
Table S18. Gene #3: 'UGT3A2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 6 | 4 | 28 |
UGT3A2 MUTATED | 0 | 1 | 2 |
UGT3A2 WILD-TYPE | 6 | 3 | 26 |
P value = 1 (Fisher's exact test), Q value = 1
Table S19. Gene #3: 'UGT3A2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 21 | 6 | 12 |
UGT3A2 MUTATED | 2 | 0 | 1 |
UGT3A2 WILD-TYPE | 19 | 6 | 11 |
P value = 0.52 (Fisher's exact test), Q value = 1
Table S20. Gene #3: 'UGT3A2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 8 | 6 | 6 |
UGT3A2 MUTATED | 1 | 1 | 0 | 1 |
UGT3A2 WILD-TYPE | 18 | 7 | 6 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
Table S21. Gene #3: 'UGT3A2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 6 | 7 |
UGT3A2 MUTATED | 3 | 0 | 0 |
UGT3A2 WILD-TYPE | 23 | 6 | 7 |
P value = 0.42 (Fisher's exact test), Q value = 1
Table S22. Gene #3: 'UGT3A2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 4 | 25 | 10 |
UGT3A2 MUTATED | 1 | 2 | 0 |
UGT3A2 WILD-TYPE | 3 | 23 | 10 |
P value = 0.0426 (Fisher's exact test), Q value = 1
Table S23. Gene #4: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 15 | 9 | 12 |
MAPK1 MUTATED | 0 | 0 | 3 |
MAPK1 WILD-TYPE | 15 | 9 | 9 |
Figure S2. Get High-res Image Gene #4: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.647 (Chi-square test), Q value = 1
Table S24. Gene #4: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 11 | 6 | 7 | 7 | 5 | 1 | 2 |
MAPK1 MUTATED | 2 | 1 | 0 | 0 | 0 | 0 | 0 |
MAPK1 WILD-TYPE | 9 | 5 | 7 | 7 | 5 | 1 | 2 |
P value = 0.667 (Chi-square test), Q value = 1
Table S25. Gene #4: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 15 | 5 | 5 | 7 | 6 |
MAPK1 MUTATED | 1 | 0 | 1 | 1 | 0 |
MAPK1 WILD-TYPE | 14 | 5 | 4 | 6 | 6 |
P value = 1 (Fisher's exact test), Q value = 1
Table S26. Gene #4: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 6 | 4 | 28 |
MAPK1 MUTATED | 0 | 0 | 3 |
MAPK1 WILD-TYPE | 6 | 4 | 25 |
P value = 0.407 (Fisher's exact test), Q value = 1
Table S27. Gene #4: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 21 | 6 | 12 |
MAPK1 MUTATED | 3 | 0 | 0 |
MAPK1 WILD-TYPE | 18 | 6 | 12 |
P value = 1 (Fisher's exact test), Q value = 1
Table S28. Gene #4: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 8 | 6 | 6 |
MAPK1 MUTATED | 2 | 1 | 0 | 0 |
MAPK1 WILD-TYPE | 17 | 7 | 6 | 6 |
P value = 1 (Fisher's exact test), Q value = 1
Table S29. Gene #4: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 6 | 7 |
MAPK1 MUTATED | 3 | 0 | 0 |
MAPK1 WILD-TYPE | 23 | 6 | 7 |
P value = 0.672 (Fisher's exact test), Q value = 1
Table S30. Gene #4: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 4 | 25 | 10 |
MAPK1 MUTATED | 0 | 3 | 0 |
MAPK1 WILD-TYPE | 4 | 22 | 10 |
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Mutation data file = transformed.cor.cli.txt
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Molecular subtypes file = CESC-TP.transferedmergedcluster.txt
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Number of patients = 39
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Number of significantly mutated genes = 4
-
Number of Molecular subtypes = 8
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Exclude genes that fewer than K tumors have mutations, K = 3
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
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
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.
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.