Correlation between gene mutation status and molecular subtypes
Uterine Carcinosarcoma (Primary solid tumor)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1WQ02R2
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/C1WQ02R2
Overview
Introduction

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

Summary

Testing the association between mutation status of 13 genes and 8 molecular subtypes across 57 patients, 2 significant findings detected with P value < 0.05 and Q value < 0.25.

- PTEN mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 13 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, 2 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 | 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
PTEN | 11 (19%) | 46 | 0.0948 (1.00) | 5e-05 (0.0052) | 0.0024 (0.247) | 0.0457 (1.00) | 0.0934 (1.00) | 0.0622 (1.00) | 0.00335 (0.342) | 0.0138 (1.00)
TP53 | 51 (89%) | 6 | 0.57 (1.00) | 0.628 (1.00) | 0.878 (1.00) | 0.515 (1.00) | 1 (1.00) | 0.912 (1.00) | 1 (1.00) | 1 (1.00)
FBXW7 | 22 (39%) | 35 | 0.262 (1.00) | 0.724 (1.00) | 0.633 (1.00) | 0.103 (1.00) | 0.467 (1.00) | 0.93 (1.00) | 1 (1.00) | 0.774 (1.00)
PPP2R1A | 16 (28%) | 41 | 0.759 (1.00) | 0.71 (1.00) | 0.591 (1.00) | 0.672 (1.00) | 0.564 (1.00) | 0.314 (1.00) | 0.698 (1.00) | 0.238 (1.00)
KRAS | 7 (12%) | 50 | 0.103 (1.00) | 0.0141 (1.00) | 0.0316 (1.00) | 0.00625 (0.625) | 0.461 (1.00) | 0.0905 (1.00) | 0.308 (1.00) | 0.0582 (1.00)
ZBTB7B | 6 (11%) | 51 | 0.724 (1.00) | 0.939 (1.00) | 1 (1.00) | 0.914 (1.00) | 0.099 (1.00) | 0.145 (1.00) | 0.48 (1.00) | 0.164 (1.00)
CHD4 | 10 (18%) | 47 | 0.346 (1.00) | 0.0104 (1.00) | 0.184 (1.00) | 0.0059 (0.596) | 0.482 (1.00) | 0.412 (1.00) | 0.0897 (1.00) | 0.214 (1.00)
PIK3R1 | 6 (11%) | 51 | 1 (1.00) | 0.94 (1.00) | 0.545 (1.00) | 0.702 (1.00) | 0.427 (1.00) | 0.508 (1.00) | 1 (1.00) | 0.305 (1.00)
ARHGAP35 | 6 (11%) | 51 | 0.567 (1.00) | 0.332 (1.00) | 1 (1.00) | 0.401 (1.00) | 1 (1.00) | 0.192 (1.00) | 1 (1.00) | 0.175 (1.00)
PIK3CA | 20 (35%) | 37 | 0.636 (1.00) | 0.902 (1.00) | 0.362 (1.00) | 0.371 (1.00) | 0.111 (1.00) | 0.341 (1.00) | 0.193 (1.00) | 0.269 (1.00)
MAMLD1 | 4 (7%) | 53 | 1 (1.00) | 0.903 (1.00) | 0.687 (1.00) | 0.771 (1.00) | 0.0669 (1.00) | 0.677 (1.00) | 0.155 (1.00) | 0.358 (1.00)
RB1 | 6 (11%) | 51 | 0.229 (1.00) | 0.0917 (1.00) | 0.0798 (1.00) | 0.0984 (1.00) | 0.834 (1.00) | 0.861 (1.00) | 0.865 (1.00) | 1 (1.00)
LYPLA2 | 3 (5%) | 54 | 0.77 (1.00) | 0.617 (1.00) | 0.678 (1.00) | 0.346 (1.00) | 0.379 (1.00) | 0.564 (1.00) | 1 (1.00) | 0.694 (1.00)

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.57 (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 | 18 | 21 | 17
TP53 MUTATED | 17 | 19 | 14
TP53 WILD-TYPE | 1 | 2 | 3

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.628 (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 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
TP53 MUTATED | 12 | 8 | 8 | 12 | 11
TP53 WILD-TYPE | 0 | 1 | 2 | 1 | 2

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.878 (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 | 15 | 20 | 12 | 10
TP53 MUTATED | 14 | 18 | 10 | 9
TP53 WILD-TYPE | 1 | 2 | 2 | 1

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.515 (Fisher's exact test), Q value = 1

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 | 11 | 4 | 8 | 6 | 8 | 6 | 14
TP53 MUTATED | 11 | 3 | 8 | 5 | 7 | 5 | 12
TP53 WILD-TYPE | 0 | 1 | 0 | 1 | 1 | 1 | 2

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (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 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
TP53 MUTATED | 10 | 20 | 4 | 17
TP53 WILD-TYPE | 1 | 2 | 0 | 2

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.912 (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
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
TP53 MUTATED | 21 | 8 | 16 | 6
TP53 WILD-TYPE | 3 | 0 | 2 | 0

'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 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
TP53 MUTATED | 12 | 21 | 18
TP53 WILD-TYPE | 1 | 2 | 2

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (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
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
TP53 MUTATED | 22 | 7 | 15 | 7
TP53 WILD-TYPE | 3 | 0 | 2 | 0

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 1

Table S9. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
FBXW7 MUTATED | 9 | 9 | 4
FBXW7 WILD-TYPE | 9 | 12 | 13

'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S10. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
FBXW7 MUTATED | 6 | 4 | 4 | 3 | 5
FBXW7 WILD-TYPE | 6 | 5 | 6 | 10 | 8

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.633 (Fisher's exact test), Q value = 1

Table S11. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
FBXW7 MUTATED | 7 | 8 | 5 | 2
FBXW7 WILD-TYPE | 8 | 12 | 7 | 8

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 1

Table S12. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
FBXW7 MUTATED | 4 | 4 | 5 | 2 | 2 | 2 | 3
FBXW7 WILD-TYPE | 7 | 0 | 3 | 4 | 6 | 4 | 11

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
FBXW7 MUTATED | 5 | 8 | 3 | 6
FBXW7 WILD-TYPE | 6 | 14 | 1 | 13

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S14. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
FBXW7 MUTATED | 9 | 4 | 7 | 2
FBXW7 WILD-TYPE | 15 | 4 | 11 | 4

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S15. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
FBXW7 MUTATED | 5 | 9 | 8
FBXW7 WILD-TYPE | 8 | 14 | 12

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.774 (Fisher's exact test), Q value = 1

Table S16. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
FBXW7 MUTATED | 9 | 4 | 6 | 3
FBXW7 WILD-TYPE | 16 | 3 | 11 | 4

'PPP2R1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.759 (Fisher's exact test), Q value = 1

Table S17. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
PPP2R1A MUTATED | 4 | 7 | 5
PPP2R1A WILD-TYPE | 14 | 14 | 12

'PPP2R1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.71 (Fisher's exact test), Q value = 1

Table S18. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
PPP2R1A MUTATED | 4 | 3 | 4 | 3 | 2
PPP2R1A WILD-TYPE | 8 | 6 | 6 | 10 | 11

'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.591 (Fisher's exact test), Q value = 1

Table S19. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
PPP2R1A MUTATED | 6 | 5 | 2 | 3
PPP2R1A WILD-TYPE | 9 | 15 | 10 | 7

'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.672 (Fisher's exact test), Q value = 1

Table S20. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
PPP2R1A MUTATED | 4 | 1 | 4 | 1 | 2 | 2 | 2
PPP2R1A WILD-TYPE | 7 | 3 | 4 | 5 | 6 | 4 | 12

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.564 (Fisher's exact test), Q value = 1

Table S21. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
PPP2R1A MUTATED | 5 | 5 | 1 | 5
PPP2R1A WILD-TYPE | 6 | 17 | 3 | 14

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.314 (Fisher's exact test), Q value = 1

Table S22. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
PPP2R1A MUTATED | 8 | 4 | 3 | 1
PPP2R1A WILD-TYPE | 16 | 4 | 15 | 5

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.698 (Fisher's exact test), Q value = 1

Table S23. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
PPP2R1A MUTATED | 5 | 6 | 5
PPP2R1A WILD-TYPE | 8 | 17 | 15

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.238 (Fisher's exact test), Q value = 1

Table S24. Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
PPP2R1A MUTATED | 8 | 4 | 3 | 1
PPP2R1A WILD-TYPE | 17 | 3 | 14 | 6

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0948 (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 | 18 | 21 | 17
PTEN MUTATED | 1 | 7 | 3
PTEN WILD-TYPE | 17 | 14 | 14

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0052

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
PTEN MUTATED | 0 | 0 | 6 | 5 | 0
PTEN WILD-TYPE | 12 | 9 | 4 | 8 | 13

Figure S1. Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0024 (Fisher's exact test), Q value = 0.25

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
PTEN MUTATED | 0 | 8 | 0 | 3
PTEN WILD-TYPE | 15 | 12 | 12 | 7

Figure S2. Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0457 (Fisher's exact 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 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
PTEN MUTATED | 0 | 0 | 3 | 0 | 3 | 0 | 5
PTEN WILD-TYPE | 11 | 4 | 5 | 6 | 5 | 6 | 9

Figure S3. Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0934 (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 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
PTEN MUTATED | 2 | 1 | 1 | 6
PTEN WILD-TYPE | 9 | 21 | 3 | 13

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0622 (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 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
PTEN MUTATED | 8 | 0 | 1 | 1
PTEN WILD-TYPE | 16 | 8 | 17 | 5

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 0.34

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
PTEN MUTATED | 3 | 0 | 7
PTEN WILD-TYPE | 10 | 23 | 13

Figure S4. 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 = 0.0138 (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 | 25 | 7 | 17 | 7
PTEN MUTATED | 8 | 0 | 0 | 2
PTEN WILD-TYPE | 17 | 7 | 17 | 5

Figure S5. Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
KRAS MUTATED | 2 | 5 | 0
KRAS WILD-TYPE | 16 | 16 | 17

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
KRAS MUTATED | 0 | 1 | 1 | 0 | 5
KRAS WILD-TYPE | 12 | 8 | 9 | 13 | 8

Figure S6. Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
KRAS MUTATED | 0 | 3 | 4 | 0
KRAS WILD-TYPE | 15 | 17 | 8 | 10

Figure S7. Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00625 (Fisher's exact test), Q value = 0.62

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
KRAS MUTATED | 0 | 0 | 1 | 0 | 0 | 4 | 2
KRAS WILD-TYPE | 11 | 4 | 7 | 6 | 8 | 2 | 12

Figure S8. Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.461 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
KRAS MUTATED | 1 | 4 | 1 | 1
KRAS WILD-TYPE | 10 | 18 | 3 | 18

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0905 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
KRAS MUTATED | 1 | 0 | 5 | 1
KRAS WILD-TYPE | 23 | 8 | 13 | 5

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
KRAS MUTATED | 1 | 5 | 1
KRAS WILD-TYPE | 12 | 18 | 19

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0582 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
KRAS MUTATED | 1 | 0 | 5 | 1
KRAS WILD-TYPE | 24 | 7 | 12 | 6

'ZBTB7B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S41. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
ZBTB7B MUTATED | 2 | 1 | 2
ZBTB7B WILD-TYPE | 16 | 20 | 15

'ZBTB7B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.939 (Fisher's exact test), Q value = 1

Table S42. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
ZBTB7B MUTATED | 2 | 1 | 1 | 1 | 1
ZBTB7B WILD-TYPE | 10 | 8 | 9 | 12 | 12

'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S43. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
ZBTB7B MUTATED | 2 | 2 | 1 | 1
ZBTB7B WILD-TYPE | 13 | 18 | 11 | 9

'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.914 (Fisher's exact test), Q value = 1

Table S44. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
ZBTB7B MUTATED | 2 | 0 | 0 | 0 | 1 | 1 | 2
ZBTB7B WILD-TYPE | 9 | 4 | 8 | 6 | 7 | 5 | 12

'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.099 (Fisher's exact test), Q value = 1

Table S45. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
ZBTB7B MUTATED | 1 | 1 | 2 | 2
ZBTB7B WILD-TYPE | 10 | 21 | 2 | 17

'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 1

Table S46. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
ZBTB7B MUTATED | 5 | 1 | 0 | 0
ZBTB7B WILD-TYPE | 19 | 7 | 18 | 6

'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 1

Table S47. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
ZBTB7B MUTATED | 2 | 1 | 3
ZBTB7B WILD-TYPE | 11 | 22 | 17

'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.164 (Fisher's exact test), Q value = 1

Table S48. Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
ZBTB7B MUTATED | 5 | 1 | 0 | 0
ZBTB7B WILD-TYPE | 20 | 6 | 17 | 7

'CHD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 1

Table S49. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
CHD4 MUTATED | 2 | 6 | 2
CHD4 WILD-TYPE | 16 | 15 | 15

'CHD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 1

Table S50. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
CHD4 MUTATED | 0 | 4 | 4 | 1 | 1
CHD4 WILD-TYPE | 12 | 5 | 6 | 12 | 12

Figure S9. Get High-res Image Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CHD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 1

Table S51. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
CHD4 MUTATED | 2 | 5 | 0 | 3
CHD4 WILD-TYPE | 13 | 15 | 12 | 7

'CHD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0059 (Fisher's exact test), Q value = 0.6

Table S52. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
CHD4 MUTATED | 0 | 2 | 4 | 0 | 3 | 0 | 1
CHD4 WILD-TYPE | 11 | 2 | 4 | 6 | 5 | 6 | 13

Figure S10. Get High-res Image Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CHD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 1

Table S53. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
CHD4 MUTATED | 3 | 2 | 1 | 3
CHD4 WILD-TYPE | 8 | 20 | 3 | 16

'CHD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.412 (Fisher's exact test), Q value = 1

Table S54. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
CHD4 MUTATED | 6 | 0 | 2 | 1
CHD4 WILD-TYPE | 18 | 8 | 16 | 5

'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0897 (Fisher's exact test), Q value = 1

Table S55. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
CHD4 MUTATED | 4 | 1 | 4
CHD4 WILD-TYPE | 9 | 22 | 16

'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.214 (Fisher's exact test), Q value = 1

Table S56. Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
CHD4 MUTATED | 6 | 0 | 1 | 2
CHD4 WILD-TYPE | 19 | 7 | 16 | 5

'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S57. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
PIK3R1 MUTATED | 2 | 2 | 2
PIK3R1 WILD-TYPE | 16 | 19 | 15

'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.94 (Fisher's exact test), Q value = 1

Table S58. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
PIK3R1 MUTATED | 2 | 1 | 1 | 1 | 1
PIK3R1 WILD-TYPE | 10 | 8 | 9 | 12 | 12

'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.545 (Fisher's exact test), Q value = 1

Table S59. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
PIK3R1 MUTATED | 3 | 2 | 1 | 0
PIK3R1 WILD-TYPE | 12 | 18 | 11 | 10

'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.702 (Fisher's exact test), Q value = 1

Table S60. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
PIK3R1 MUTATED | 2 | 1 | 1 | 0 | 0 | 1 | 1
PIK3R1 WILD-TYPE | 9 | 3 | 7 | 6 | 8 | 5 | 13

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 1

Table S61. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
PIK3R1 MUTATED | 2 | 2 | 1 | 1
PIK3R1 WILD-TYPE | 9 | 20 | 3 | 18

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.508 (Fisher's exact test), Q value = 1

Table S62. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
PIK3R1 MUTATED | 2 | 2 | 2 | 0
PIK3R1 WILD-TYPE | 22 | 6 | 16 | 6

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S63. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
PIK3R1 MUTATED | 1 | 3 | 2
PIK3R1 WILD-TYPE | 12 | 20 | 18

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.305 (Fisher's exact test), Q value = 1

Table S64. Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
PIK3R1 MUTATED | 2 | 2 | 1 | 1
PIK3R1 WILD-TYPE | 23 | 5 | 16 | 6

'ARHGAP35 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.567 (Fisher's exact test), Q value = 1

Table S65. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
ARHGAP35 MUTATED | 1 | 2 | 3
ARHGAP35 WILD-TYPE | 17 | 19 | 14

'ARHGAP35 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.332 (Fisher's exact test), Q value = 1

Table S66. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
ARHGAP35 MUTATED | 2 | 0 | 2 | 0 | 2
ARHGAP35 WILD-TYPE | 10 | 9 | 8 | 13 | 11

'ARHGAP35 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S67. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
ARHGAP35 MUTATED | 2 | 2 | 1 | 1
ARHGAP35 WILD-TYPE | 13 | 18 | 11 | 9

'ARHGAP35 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.401 (Fisher's exact test), Q value = 1

Table S68. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
ARHGAP35 MUTATED | 2 | 0 | 2 | 0 | 1 | 1 | 0
ARHGAP35 WILD-TYPE | 9 | 4 | 6 | 6 | 7 | 5 | 14

'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S69. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
ARHGAP35 MUTATED | 1 | 2 | 0 | 2
ARHGAP35 WILD-TYPE | 10 | 20 | 4 | 17

'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.192 (Fisher's exact test), Q value = 1

Table S70. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
ARHGAP35 MUTATED | 1 | 2 | 1 | 1
ARHGAP35 WILD-TYPE | 23 | 6 | 17 | 5

'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S71. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
ARHGAP35 MUTATED | 1 | 2 | 2
ARHGAP35 WILD-TYPE | 12 | 21 | 18

'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.175 (Fisher's exact test), Q value = 1

Table S72. Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
ARHGAP35 MUTATED | 1 | 2 | 1 | 1
ARHGAP35 WILD-TYPE | 24 | 5 | 16 | 6

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.636 (Fisher's exact test), Q value = 1

Table S73. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
PIK3CA MUTATED | 5 | 9 | 5
PIK3CA WILD-TYPE | 13 | 12 | 12

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.902 (Fisher's exact test), Q value = 1

Table S74. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
PIK3CA MUTATED | 4 | 3 | 5 | 4 | 4
PIK3CA WILD-TYPE | 8 | 6 | 5 | 9 | 9

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.362 (Fisher's exact test), Q value = 1

Table S75. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
PIK3CA MUTATED | 5 | 10 | 3 | 2
PIK3CA WILD-TYPE | 10 | 10 | 9 | 8

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.371 (Fisher's exact test), Q value = 1

Table S76. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
PIK3CA MUTATED | 3 | 3 | 4 | 2 | 1 | 1 | 6
PIK3CA WILD-TYPE | 8 | 1 | 4 | 4 | 7 | 5 | 8

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 1

Table S77. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
PIK3CA MUTATED | 4 | 4 | 2 | 10
PIK3CA WILD-TYPE | 7 | 18 | 2 | 9

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.341 (Fisher's exact test), Q value = 1

Table S78. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
PIK3CA MUTATED | 11 | 2 | 4 | 3
PIK3CA WILD-TYPE | 13 | 6 | 14 | 3

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.193 (Fisher's exact test), Q value = 1

Table S79. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
PIK3CA MUTATED | 6 | 5 | 9
PIK3CA WILD-TYPE | 7 | 18 | 11

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.269 (Fisher's exact test), Q value = 1

Table S80. Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
PIK3CA MUTATED | 12 | 1 | 4 | 3
PIK3CA WILD-TYPE | 13 | 6 | 13 | 4

'MAMLD1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S81. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
MAMLD1 MUTATED | 1 | 2 | 1
MAMLD1 WILD-TYPE | 17 | 19 | 16

'MAMLD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S82. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
MAMLD1 MUTATED | 0 | 1 | 1 | 1 | 1
MAMLD1 WILD-TYPE | 12 | 8 | 9 | 12 | 12

'MAMLD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S83. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
MAMLD1 MUTATED | 0 | 2 | 1 | 1
MAMLD1 WILD-TYPE | 15 | 18 | 11 | 9

'MAMLD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.771 (Fisher's exact test), Q value = 1

Table S84. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
MAMLD1 MUTATED | 0 | 0 | 1 | 1 | 1 | 0 | 1
MAMLD1 WILD-TYPE | 11 | 4 | 7 | 5 | 7 | 6 | 13

'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0669 (Fisher's exact test), Q value = 1

Table S85. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
MAMLD1 MUTATED | 0 | 0 | 1 | 3
MAMLD1 WILD-TYPE | 11 | 22 | 3 | 16

'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.677 (Fisher's exact test), Q value = 1

Table S86. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
MAMLD1 MUTATED | 2 | 0 | 1 | 1
MAMLD1 WILD-TYPE | 22 | 8 | 17 | 5

'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 1

Table S87. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
MAMLD1 MUTATED | 2 | 0 | 2
MAMLD1 WILD-TYPE | 11 | 23 | 18

'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.358 (Fisher's exact test), Q value = 1

Table S88. Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
MAMLD1 MUTATED | 3 | 0 | 0 | 1
MAMLD1 WILD-TYPE | 22 | 7 | 17 | 6

'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 1

Table S89. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
RB1 MUTATED | 2 | 4 | 0
RB1 WILD-TYPE | 16 | 17 | 17

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0917 (Fisher's exact test), Q value = 1

Table S90. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
RB1 MUTATED | 0 | 1 | 3 | 2 | 0
RB1 WILD-TYPE | 12 | 8 | 7 | 11 | 13

'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0798 (Fisher's exact test), Q value = 1

Table S91. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
RB1 MUTATED | 0 | 4 | 0 | 2
RB1 WILD-TYPE | 15 | 16 | 12 | 8

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0984 (Fisher's exact test), Q value = 1

Table S92. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
RB1 MUTATED | 0 | 0 | 2 | 0 | 3 | 0 | 1
RB1 WILD-TYPE | 11 | 4 | 6 | 6 | 5 | 6 | 13

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S93. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
RB1 MUTATED | 2 | 2 | 0 | 2
RB1 WILD-TYPE | 9 | 20 | 4 | 17

'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.861 (Fisher's exact test), Q value = 1

Table S94. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
RB1 MUTATED | 3 | 0 | 2 | 1
RB1 WILD-TYPE | 21 | 8 | 16 | 5

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.865 (Fisher's exact test), Q value = 1

Table S95. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
RB1 MUTATED | 2 | 2 | 2
RB1 WILD-TYPE | 11 | 21 | 18

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S96. Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
RB1 MUTATED | 3 | 0 | 2 | 1
RB1 WILD-TYPE | 22 | 7 | 15 | 6

'LYPLA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.77 (Fisher's exact test), Q value = 1

Table S97. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 18 | 21 | 17
LYPLA2 MUTATED | 1 | 2 | 0
LYPLA2 WILD-TYPE | 17 | 19 | 17

'LYPLA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.617 (Fisher's exact test), Q value = 1

Table S98. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 12 | 9 | 10 | 13 | 13
LYPLA2 MUTATED | 0 | 1 | 1 | 0 | 1
LYPLA2 WILD-TYPE | 12 | 8 | 9 | 13 | 12

'LYPLA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.678 (Fisher's exact test), Q value = 1

Table S99. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 20 | 12 | 10
LYPLA2 MUTATED | 0 | 1 | 1 | 1
LYPLA2 WILD-TYPE | 15 | 19 | 11 | 9

'LYPLA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.346 (Fisher's exact test), Q value = 1

Table S100. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 11 | 4 | 8 | 6 | 8 | 6 | 14
LYPLA2 MUTATED | 0 | 0 | 1 | 0 | 1 | 1 | 0
LYPLA2 WILD-TYPE | 11 | 4 | 7 | 6 | 7 | 5 | 14

'LYPLA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 1

Table S101. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 22 | 4 | 19
LYPLA2 MUTATED | 0 | 1 | 1 | 1
LYPLA2 WILD-TYPE | 11 | 21 | 3 | 18

'LYPLA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.564 (Fisher's exact test), Q value = 1

Table S102. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 8 | 18 | 6
LYPLA2 MUTATED | 1 | 0 | 1 | 1
LYPLA2 WILD-TYPE | 23 | 8 | 17 | 5

'LYPLA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S103. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 13 | 23 | 20
LYPLA2 MUTATED | 1 | 1 | 1
LYPLA2 WILD-TYPE | 12 | 22 | 19

'LYPLA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.694 (Fisher's exact test), Q value = 1

Table S104. Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 25 | 7 | 17 | 7
LYPLA2 MUTATED | 1 | 0 | 1 | 1
LYPLA2 WILD-TYPE | 24 | 7 | 16 | 6

Methods & Data
Input

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

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

- Number of patients = 57

- Number of significantly mutated genes = 13

- 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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