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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