Correlation between gene mutation status and molecular subtypes
Lung Adenocarcinoma (Primary solid tumor)
17 April 2019 | None
Maintainer Information
Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)
Overview
Introduction

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

Summary

Testing the association between mutation status of 19 genes and 2 molecular subtypes across 108 patients, 12 significant findings detected with P value < 0.05 and Q value < 0.25.

- TP53 mutation correlated to 'LINCRNA_CHIERARCHICAL'.

- KRAS mutation correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- STK11 mutation correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- EGFR mutation correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

- LMO2 mutation correlated to 'MRNA_CHIERARCHICAL'.

- C10ORF62 mutation correlated to 'MRNA_CHIERARCHICAL'.

- BIRC6 mutation correlated to 'MRNA_CHIERARCHICAL'.

- C16ORF82 mutation correlated to 'MRNA_CHIERARCHICAL'.

- CLIP2 mutation correlated to 'MRNA_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 19 genes and 2 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 12 significant findings detected.

|  | Clinical Features | MRNA CHIERARCHICAL | LINCRNA CHIERARCHICAL
| nMutated (%) | nWild-Type | Fisher's exact test | Fisher's exact test
KRAS | 34 (31%) | 74 | 2e-05 (0.000127) | 2e-05 (0.000127)
STK11 | 20 (19%) | 88 | 1e-05 (9.5e-05) | 1e-05 (9.5e-05)
EGFR | 37 (34%) | 71 | 1e-05 (9.5e-05) | 1e-05 (9.5e-05)
TP53 | 59 (55%) | 49 | 0.0665 (0.194) | 0.0362 (0.115)
LMO2 | 5 (5%) | 103 | 0.0353 (0.115) | 0.327 (0.547)
C10ORF62 | 4 (4%) | 104 | 0.0265 (0.112) | 0.688 (0.747)
BIRC6 | 6 (6%) | 102 | 0.0105 (0.0572) | 0.372 (0.547)
C16ORF82 | 5 (5%) | 103 | 0.0356 (0.115) | 0.0774 (0.21)
CLIP2 | 7 (6%) | 101 | 0.0244 (0.112) | 0.223 (0.474)
KEAP1 | 12 (11%) | 96 | 0.36 (0.547) | 0.684 (0.747)
RB1 | 8 (7%) | 100 | 0.643 (0.747) | 0.807 (0.852)
IL21R | 6 (6%) | 102 | 0.232 (0.474) | 0.372 (0.547)
EGFL6 | 5 (5%) | 103 | 0.511 (0.647) | 0.601 (0.737)
DKK3 | 4 (4%) | 104 | 0.459 (0.602) | 0.686 (0.747)
TDG | 3 (3%) | 105 | 0.237 (0.474) | 0.358 (0.547)
GRIK3 | 9 (8%) | 99 | 0.321 (0.547) | 0.416 (0.586)
AFAP1 | 5 (5%) | 103 | 0.374 (0.547) | 0.445 (0.602)
ELFN1 | 6 (6%) | 102 | 1 (1.00) | 1 (1.00)
TLR7 | 6 (6%) | 102 | 0.232 (0.474) | 0.0993 (0.252)

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0665 (Fisher's exact test), Q value = 0.19

Table S1. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
TP53 MUTATED | 18 | 19 | 22
TP53 WILD-TYPE | 15 | 7 | 27

'TP53 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 0.11

Table S2. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
TP53 MUTATED | 17 | 22 | 20
TP53 WILD-TYPE | 15 | 8 | 26

Figure S1. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S3. Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
KRAS MUTATED | 18 | 11 | 5
KRAS WILD-TYPE | 15 | 15 | 44

Figure S2. Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S4. Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
KRAS MUTATED | 18 | 12 | 4
KRAS WILD-TYPE | 14 | 18 | 42

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

'STK11 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S5. Gene #3: 'STK11 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
STK11 MUTATED | 18 | 1 | 1
STK11 WILD-TYPE | 15 | 25 | 48

Figure S4. Get High-res Image Gene #3: 'STK11 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'STK11 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S6. Gene #3: 'STK11 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
STK11 MUTATED | 19 | 0 | 1
STK11 WILD-TYPE | 13 | 30 | 45

Figure S5. Get High-res Image Gene #3: 'STK11 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S7. Gene #4: 'EGFR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
EGFR MUTATED | 1 | 7 | 29
EGFR WILD-TYPE | 32 | 19 | 20

Figure S6. Get High-res Image Gene #4: 'EGFR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S8. Gene #4: 'EGFR MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
EGFR MUTATED | 0 | 10 | 27
EGFR WILD-TYPE | 32 | 20 | 19

Figure S7. Get High-res Image Gene #4: 'EGFR MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.36 (Fisher's exact test), Q value = 0.55

Table S9. Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
KEAP1 MUTATED | 6 | 2 | 4
KEAP1 WILD-TYPE | 27 | 24 | 45

'KEAP1 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.684 (Fisher's exact test), Q value = 0.75

Table S10. Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
KEAP1 MUTATED | 5 | 3 | 4
KEAP1 WILD-TYPE | 27 | 27 | 42

'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.643 (Fisher's exact test), Q value = 0.75

Table S11. Gene #6: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
RB1 MUTATED | 2 | 3 | 3
RB1 WILD-TYPE | 31 | 23 | 46

'RB1 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.807 (Fisher's exact test), Q value = 0.85

Table S12. Gene #6: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
RB1 MUTATED | 2 | 3 | 3
RB1 WILD-TYPE | 30 | 27 | 43

'IL21R MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 0.47

Table S13. Gene #7: 'IL21R MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
IL21R MUTATED | 2 | 3 | 1
IL21R WILD-TYPE | 31 | 23 | 48

'IL21R MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.372 (Fisher's exact test), Q value = 0.55

Table S14. Gene #7: 'IL21R MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
IL21R MUTATED | 2 | 3 | 1
IL21R WILD-TYPE | 30 | 27 | 45

'EGFL6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.511 (Fisher's exact test), Q value = 0.65

Table S15. Gene #8: 'EGFL6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
EGFL6 MUTATED | 2 | 2 | 1
EGFL6 WILD-TYPE | 31 | 24 | 48

'EGFL6 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.601 (Fisher's exact test), Q value = 0.74

Table S16. Gene #8: 'EGFL6 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
EGFL6 MUTATED | 2 | 2 | 1
EGFL6 WILD-TYPE | 30 | 28 | 45

'LMO2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0353 (Fisher's exact test), Q value = 0.11

Table S17. Gene #9: 'LMO2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
LMO2 MUTATED | 2 | 3 | 0
LMO2 WILD-TYPE | 31 | 23 | 49

Figure S8. Get High-res Image Gene #9: 'LMO2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'LMO2 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.327 (Fisher's exact test), Q value = 0.55

Table S18. Gene #9: 'LMO2 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
LMO2 MUTATED | 1 | 3 | 1
LMO2 WILD-TYPE | 31 | 27 | 45

'C10ORF62 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.11

Table S19. Gene #10: 'C10ORF62 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
C10ORF62 MUTATED | 1 | 3 | 0
C10ORF62 WILD-TYPE | 32 | 23 | 49

Figure S9. Get High-res Image Gene #10: 'C10ORF62 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'C10ORF62 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.688 (Fisher's exact test), Q value = 0.75

Table S20. Gene #10: 'C10ORF62 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
C10ORF62 MUTATED | 1 | 2 | 1
C10ORF62 WILD-TYPE | 31 | 28 | 45

'DKK3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 0.6

Table S21. Gene #11: 'DKK3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
DKK3 MUTATED | 1 | 2 | 1
DKK3 WILD-TYPE | 32 | 24 | 48

'DKK3 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.686 (Fisher's exact test), Q value = 0.75

Table S22. Gene #11: 'DKK3 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
DKK3 MUTATED | 1 | 2 | 1
DKK3 WILD-TYPE | 31 | 28 | 45

'BIRC6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.057

Table S23. Gene #12: 'BIRC6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
BIRC6 MUTATED | 2 | 4 | 0
BIRC6 WILD-TYPE | 31 | 22 | 49

Figure S10. Get High-res Image Gene #12: 'BIRC6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'BIRC6 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.372 (Fisher's exact test), Q value = 0.55

Table S24. Gene #12: 'BIRC6 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
BIRC6 MUTATED | 2 | 3 | 1
BIRC6 WILD-TYPE | 30 | 27 | 45

'TDG MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.237 (Fisher's exact test), Q value = 0.47

Table S25. Gene #13: 'TDG MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
TDG MUTATED | 0 | 2 | 1
TDG WILD-TYPE | 33 | 24 | 48

'TDG MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.358 (Fisher's exact test), Q value = 0.55

Table S26. Gene #13: 'TDG MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
TDG MUTATED | 0 | 2 | 1
TDG WILD-TYPE | 32 | 28 | 45

'C16ORF82 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0356 (Fisher's exact test), Q value = 0.11

Table S27. Gene #14: 'C16ORF82 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
C16ORF82 MUTATED | 2 | 3 | 0
C16ORF82 WILD-TYPE | 31 | 23 | 49

Figure S11. Get High-res Image Gene #14: 'C16ORF82 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'C16ORF82 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0774 (Fisher's exact test), Q value = 0.21

Table S28. Gene #14: 'C16ORF82 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
C16ORF82 MUTATED | 2 | 3 | 0
C16ORF82 WILD-TYPE | 30 | 27 | 46

'GRIK3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.321 (Fisher's exact test), Q value = 0.55

Table S29. Gene #15: 'GRIK3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
GRIK3 MUTATED | 4 | 3 | 2
GRIK3 WILD-TYPE | 29 | 23 | 47

'GRIK3 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.416 (Fisher's exact test), Q value = 0.59

Table S30. Gene #15: 'GRIK3 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
GRIK3 MUTATED | 4 | 3 | 2
GRIK3 WILD-TYPE | 28 | 27 | 44

'AFAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 0.55

Table S31. Gene #16: 'AFAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
AFAP1 MUTATED | 3 | 1 | 1
AFAP1 WILD-TYPE | 30 | 25 | 48

'AFAP1 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.445 (Fisher's exact test), Q value = 0.6

Table S32. Gene #16: 'AFAP1 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
AFAP1 MUTATED | 3 | 1 | 1
AFAP1 WILD-TYPE | 29 | 29 | 45

'CLIP2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.11

Table S33. Gene #17: 'CLIP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
CLIP2 MUTATED | 4 | 3 | 0
CLIP2 WILD-TYPE | 29 | 23 | 49

Figure S12. Get High-res Image Gene #17: 'CLIP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'CLIP2 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.223 (Fisher's exact test), Q value = 0.47

Table S34. Gene #17: 'CLIP2 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
CLIP2 MUTATED | 4 | 2 | 1
CLIP2 WILD-TYPE | 28 | 28 | 45

'ELFN1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S35. Gene #18: 'ELFN1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
ELFN1 MUTATED | 2 | 1 | 3
ELFN1 WILD-TYPE | 31 | 25 | 46

'ELFN1 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

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

Table S36. Gene #18: 'ELFN1 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
ELFN1 MUTATED | 2 | 1 | 3
ELFN1 WILD-TYPE | 30 | 29 | 43

'TLR7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 0.47

Table S37. Gene #19: 'TLR7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 26 | 49
TLR7 MUTATED | 2 | 3 | 1
TLR7 WILD-TYPE | 31 | 23 | 48

'TLR7 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0993 (Fisher's exact test), Q value = 0.25

Table S38. Gene #19: 'TLR7 MUTATION STATUS' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 30 | 46
TLR7 MUTATED | 1 | 4 | 1
TLR7 WILD-TYPE | 31 | 26 | 45

Methods & Data
Input

- Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

- Processed Mutation data file = /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/03d5323d-b92b-4a22-90d3-f871afeb0c16/correlate_genomic_events_all/ee5cbd6a-2978-41ca-ada7-5146d30af8b4/call-preprocess_genomic_event/transformed.cor.cli.txt

- Molecular subtypes file = /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/69dd18b3-97fe-4143-b0f4-32e5d55e929d/aggregate_clusters_workflow/d44c315a-761b-4b72-be1f-cb969be36102/call-aggregate_clusters/CPTAC3-LUAD-TP.transposedmergedcluster.txt

- Number of patients = 108

- Number of significantly mutated genes = 19

- Number of Molecular subtypes = 2

- 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.

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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