Correlation between gene mutation status and molecular subtypes
Uterine Carcinosarcoma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C13R0RK9
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/C13R0RK9
Overview
Introduction

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

Summary

Testing the association between mutation status of 9 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 9 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 | 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
PTEN | 11 (19%) | 46 | 0.0123 (0.833) | 0.000216 (0.0156) | 0.00212 (0.151) | 0.00433 (0.303) | 0.096 (1.00) | 0.00872 (0.602) | 0.0237 (1.00) | 0.0241 (1.00)
FBXW7 | 22 (39%) | 35 | 0.0511 (1.00) | 0.714 (1.00) | 0.595 (1.00) | 0.494 (1.00) | 0.441 (1.00) | 1 (1.00) | 0.938 (1.00) | 0.737 (1.00)
KRAS | 7 (12%) | 50 | 0.32 (1.00) | 0.0187 (1.00) | 0.0323 (1.00) | 0.0264 (1.00) | 0.463 (1.00) | 0.494 (1.00) | 0.513 (1.00) | 0.322 (1.00)
TP53 | 51 (89%) | 6 | 0.331 (1.00) | 0.591 (1.00) | 0.877 (1.00) | 0.822 (1.00) | 1 (1.00) | 0.699 (1.00) | 1 (1.00) | 1 (1.00)
PIK3CA | 20 (35%) | 37 | 0.267 (1.00) | 0.875 (1.00) | 0.365 (1.00) | 0.303 (1.00) | 0.105 (1.00) | 0.0268 (1.00) | 0.162 (1.00) | 0.0274 (1.00)
PPP2R1A | 16 (28%) | 41 | 1 (1.00) | 0.701 (1.00) | 0.584 (1.00) | 0.852 (1.00) | 0.56 (1.00) | 0.635 (1.00) | 0.234 (1.00) | 1 (1.00)
PIK3R1 | 6 (11%) | 51 | 0.856 (1.00) | 0.95 (1.00) | 0.544 (1.00) | 0.592 (1.00) | 0.425 (1.00) | 0.705 (1.00) | 0.744 (1.00) | 0.459 (1.00)
ZBTB7B | 6 (11%) | 51 | 0.483 (1.00) | 0.95 (1.00) | 1 (1.00) | 1 (1.00) | 0.0978 (1.00) | 0.197 (1.00) | 0.15 (1.00) | 0.29 (1.00)
RB1 | 6 (11%) | 51 | 0.541 (1.00) | 0.121 (1.00) | 0.08 (1.00) | 0.0401 (1.00) | 0.835 (1.00) | 0.484 (1.00) | 0.918 (1.00) | 0.712 (1.00)

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0511 (Fisher's exact test), Q value = 1

Table S1. Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 24 | 10
FBXW7 MUTATED | 12 | 9 | 1
FBXW7 WILD-TYPE | 10 | 15 | 9

'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.714 (Chi-square test), Q value = 1

Table S2. Gene #1: '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 = 0.595 (Fisher's exact test), Q value = 1

Table S3. Gene #1: '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 = 0.494 (Fisher's exact test), Q value = 1

Table S4. Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 11 | 22 | 9
FBXW7 MUTATED | 8 | 4 | 8 | 2
FBXW7 WILD-TYPE | 7 | 7 | 14 | 7

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 1

Table S5. Gene #1: '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 = 1 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 27 | 28
FBXW7 MUTATED | 0 | 11 | 11
FBXW7 WILD-TYPE | 1 | 16 | 17

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.938 (Fisher's exact test), Q value = 1

Table S7. Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 23 | 5 | 17
FBXW7 MUTATED | 5 | 9 | 2 | 6
FBXW7 WILD-TYPE | 6 | 14 | 3 | 11

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.737 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 25 | 30
FBXW7 MUTATED | 0 | 11 | 11
FBXW7 WILD-TYPE | 1 | 14 | 19

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.32 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 24 | 10
KRAS MUTATED | 2 | 5 | 0
KRAS WILD-TYPE | 20 | 19 | 10

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0187 (Chi-square test), Q value = 1

Table S10. Gene #2: '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 S1. Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 1

Table S11. Gene #2: '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 S2. Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 11 | 22 | 9
KRAS MUTATED | 0 | 4 | 3 | 0
KRAS WILD-TYPE | 15 | 7 | 19 | 9

Figure S3. Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.463 (Fisher's exact test), Q value = 1

Table S13. Gene #2: '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 = 0.494 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 27 | 28
KRAS MUTATED | 0 | 2 | 5
KRAS WILD-TYPE | 1 | 25 | 23

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.513 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 23 | 5 | 17
KRAS MUTATED | 1 | 5 | 0 | 1
KRAS WILD-TYPE | 10 | 18 | 5 | 16

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 25 | 30
KRAS MUTATED | 0 | 5 | 2
KRAS WILD-TYPE | 1 | 20 | 28

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.331 (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 | 22 | 24 | 10
TP53 MUTATED | 21 | 21 | 8
TP53 WILD-TYPE | 1 | 3 | 2

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.591 (Chi-square test), Q value = 1

Table S18. Gene #3: '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 = 0.877 (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 | 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 = 0.822 (Fisher's exact 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
--- | --- | --- | --- | ---
ALL | 15 | 11 | 22 | 9
TP53 MUTATED | 14 | 9 | 20 | 8
TP53 WILD-TYPE | 1 | 2 | 2 | 1

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (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 | 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 = 0.699 (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 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 27 | 28
TP53 MUTATED | 1 | 24 | 26
TP53 WILD-TYPE | 0 | 3 | 2

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (Fisher's exact 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
--- | --- | --- | --- | ---
ALL | 11 | 23 | 5 | 17
TP53 MUTATED | 10 | 21 | 5 | 15
TP53 WILD-TYPE | 1 | 2 | 0 | 2

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (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
--- | --- | --- | ---
ALL | 1 | 25 | 30
TP53 MUTATED | 1 | 23 | 27
TP53 WILD-TYPE | 0 | 2 | 3

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

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

Table S25. Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 24 | 10
PIK3CA MUTATED | 5 | 11 | 3
PIK3CA WILD-TYPE | 17 | 13 | 7

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.875 (Chi-square test), Q value = 1

Table S26. Gene #4: '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 = 0.365 (Fisher's exact test), Q value = 1

Table S27. Gene #4: '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 = 0.303 (Fisher's exact test), Q value = 1

Table S28. Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 11 | 22 | 9
PIK3CA MUTATED | 6 | 3 | 10 | 1
PIK3CA WILD-TYPE | 9 | 8 | 12 | 8

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 1

Table S29. Gene #4: '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 = 0.0268 (Fisher's exact test), Q value = 1

Table S30. Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 27 | 28
PIK3CA MUTATED | 1 | 13 | 6
PIK3CA WILD-TYPE | 0 | 14 | 22

Figure S4. Get High-res Image Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 1

Table S31. Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 23 | 5 | 17
PIK3CA MUTATED | 5 | 5 | 1 | 9
PIK3CA WILD-TYPE | 6 | 18 | 4 | 8

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 1

Table S32. Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 25 | 30
PIK3CA MUTATED | 1 | 5 | 14
PIK3CA WILD-TYPE | 0 | 20 | 16

Figure S5. Get High-res Image Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PPP2R1A MUTATION STATUS' versus 'CN_CNMF'

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

Table S33. Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 24 | 10
PPP2R1A MUTATED | 6 | 7 | 3
PPP2R1A WILD-TYPE | 16 | 17 | 7

'PPP2R1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.701 (Chi-square test), Q value = 1

Table S34. Gene #5: '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 = 0.584 (Fisher's exact test), Q value = 1

Table S35. Gene #5: '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 = 0.852 (Fisher's exact test), Q value = 1

Table S36. Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 11 | 22 | 9
PPP2R1A MUTATED | 5 | 2 | 6 | 3
PPP2R1A WILD-TYPE | 10 | 9 | 16 | 6

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S37. Gene #5: '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 = 0.635 (Fisher's exact test), Q value = 1

Table S38. Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 27 | 28
PPP2R1A MUTATED | 0 | 9 | 7
PPP2R1A WILD-TYPE | 1 | 18 | 21

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.234 (Fisher's exact test), Q value = 1

Table S39. Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 23 | 5 | 17
PPP2R1A MUTATED | 6 | 5 | 1 | 4
PPP2R1A WILD-TYPE | 5 | 18 | 4 | 13

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S40. Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 25 | 30
PPP2R1A MUTATED | 0 | 7 | 9
PPP2R1A WILD-TYPE | 1 | 18 | 21

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.83

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 24 | 10
PTEN MUTATED | 1 | 9 | 1
PTEN WILD-TYPE | 21 | 15 | 9

Figure S6. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000216 (Chi-square test), Q value = 0.016

Table S42. Gene #6: '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 S7. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00212 (Fisher's exact test), Q value = 0.15

Table S43. Gene #6: '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 S8. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00433 (Fisher's exact test), Q value = 0.3

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 11 | 22 | 9
PTEN MUTATED | 0 | 0 | 8 | 3
PTEN WILD-TYPE | 15 | 11 | 14 | 6

Figure S9. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.096 (Fisher's exact test), Q value = 1

Table S45. Gene #6: '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 = 0.00872 (Fisher's exact test), Q value = 0.6

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 27 | 28
PTEN MUTATED | 0 | 9 | 1
PTEN WILD-TYPE | 1 | 18 | 27

Figure S10. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 23 | 5 | 17
PTEN MUTATED | 1 | 1 | 2 | 6
PTEN WILD-TYPE | 10 | 22 | 3 | 11

Figure S11. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0241 (Fisher's exact test), Q value = 1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 25 | 30
PTEN MUTATED | 0 | 1 | 9
PTEN WILD-TYPE | 1 | 24 | 21

Figure S12. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S49. Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 24 | 10
PIK3R1 MUTATED | 3 | 2 | 1
PIK3R1 WILD-TYPE | 19 | 22 | 9

'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.95 (Chi-square test), Q value = 1

Table S50. Gene #7: '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 = 0.544 (Fisher's exact test), Q value = 1

Table S51. Gene #7: '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 = 0.592 (Fisher's exact test), Q value = 1

Table S52. Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 11 | 22 | 9
PIK3R1 MUTATED | 3 | 1 | 2 | 0
PIK3R1 WILD-TYPE | 12 | 10 | 20 | 9

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 1

Table S53. Gene #7: '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 = 0.705 (Fisher's exact test), Q value = 1

Table S54. Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 27 | 28
PIK3R1 MUTATED | 0 | 2 | 4
PIK3R1 WILD-TYPE | 1 | 25 | 24

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.744 (Fisher's exact test), Q value = 1

Table S55. Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 23 | 5 | 17
PIK3R1 MUTATED | 2 | 3 | 0 | 1
PIK3R1 WILD-TYPE | 9 | 20 | 5 | 16

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 1

Table S56. Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 25 | 30
PIK3R1 MUTATED | 0 | 4 | 2
PIK3R1 WILD-TYPE | 1 | 21 | 28

'ZBTB7B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 1

Table S57. Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 24 | 10
ZBTB7B MUTATED | 3 | 1 | 1
ZBTB7B WILD-TYPE | 19 | 23 | 9

'ZBTB7B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.95 (Chi-square test), Q value = 1

Table S58. Gene #8: '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 S59. Gene #8: '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 = 1 (Fisher's exact test), Q value = 1

Table S60. Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 11 | 22 | 9
ZBTB7B MUTATED | 2 | 1 | 2 | 1
ZBTB7B WILD-TYPE | 13 | 10 | 20 | 8

'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S61. Gene #8: '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 = 0.197 (Fisher's exact test), Q value = 1

Table S62. Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 27 | 28
ZBTB7B MUTATED | 0 | 5 | 1
ZBTB7B WILD-TYPE | 1 | 22 | 27

'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 1

Table S63. Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 23 | 5 | 17
ZBTB7B MUTATED | 1 | 1 | 2 | 2
ZBTB7B WILD-TYPE | 10 | 22 | 3 | 15

'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 1

Table S64. Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 25 | 30
ZBTB7B MUTATED | 0 | 1 | 5
ZBTB7B WILD-TYPE | 1 | 24 | 25

'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S65. Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 24 | 10
RB1 MUTATED | 2 | 4 | 0
RB1 WILD-TYPE | 20 | 20 | 10

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.121 (Chi-square test), Q value = 1

Table S66. Gene #9: '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 = 0.08 (Fisher's exact test), Q value = 1

Table S67. Gene #9: '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 = 0.0401 (Fisher's exact test), Q value = 1

Table S68. Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 11 | 22 | 9
RB1 MUTATED | 0 | 0 | 3 | 3
RB1 WILD-TYPE | 15 | 11 | 19 | 6

Figure S13. Get High-res Image Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.835 (Fisher's exact test), Q value = 1

Table S69. Gene #9: '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 = 0.484 (Fisher's exact test), Q value = 1

Table S70. Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 27 | 28
RB1 MUTATED | 0 | 4 | 2
RB1 WILD-TYPE | 1 | 23 | 26

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.918 (Fisher's exact test), Q value = 1

Table S71. Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 11 | 23 | 5 | 17
RB1 MUTATED | 1 | 2 | 1 | 2
RB1 WILD-TYPE | 10 | 21 | 4 | 15

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S72. Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 1 | 25 | 30
RB1 MUTATED | 0 | 2 | 4
RB1 WILD-TYPE | 1 | 23 | 26

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 = 9

- 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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