Correlation between gene mutation status and molecular subtypes
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)
Made with Nozzle