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 26 genes and 10 molecular subtypes across 219 patients, 21 significant findings detected with P value < 0.05 and Q value < 0.25.

  • PIK3CA mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • PGM5 mutation correlated to 'METHLYATION_CNMF'.

  • CBWD1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • TP53 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • ARID1A mutation correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • RHOA mutation correlated to 'MIRSEQ_MATURE_CNMF'.

  • BCOR mutation correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 26 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 21 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		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 Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
PIK3CA 48 (22%) 171 5.42e-05
(0.0133) 		1.83e-09
(4.65e-07) 		0.0119
(1.00) 		0.000478
(0.114) 		0.000815
(0.194) 		5.05e-07
(0.000128) 		0.017
(1.00) 		0.00544
(1.00) 		0.0478
(1.00) 		0.000865
(0.205)
TP53 98 (45%) 121 9.45e-11
(2.41e-08) 		3.18e-05
(0.00792) 		0.209
(1.00) 		0.667
(1.00) 		0.000382
(0.0921) 		0.00163
(0.377) 		0.00723
(1.00) 		5.1e-06
(0.00128) 		0.286
(1.00) 		0.000325
(0.0786)
CBWD1 28 (13%) 191 9.54e-05
(0.0232) 		1.79e-06
(0.000452) 		5.26e-05
(0.013) 		0.00312
(0.699) 		0.00122
(0.286) 		0.00844
(1.00) 		0.0309
(1.00) 		0.00232
(0.528) 		0.178
(1.00) 		0.00237
(0.537)
ARID1A 41 (19%) 178 6.15e-05
(0.0151) 		0.00262
(0.591) 		0.0122
(1.00) 		0.19
(1.00) 		0.00097
(0.229) 		1.85e-05
(0.00463) 		0.0423
(1.00) 		0.0392
(1.00) 		0.679
(1.00) 		0.297
(1.00)
BCOR 16 (7%) 203 0.00518
(1.00) 		6.67e-05
(0.0163) 		0.147
(1.00) 		0.0109
(1.00) 		0.0583
(1.00) 		0.0234
(1.00) 		0.0129
(1.00) 		0.000453
(0.109) 		0.273
(1.00) 		0.151
(1.00)
PGM5 22 (10%) 197 0.00223
(0.51) 		4.28e-05
(0.0106) 		0.159
(1.00) 		0.0601
(1.00) 		0.00267
(0.601) 		0.0046
(1.00) 		0.264
(1.00) 		0.0242
(1.00) 		0.0857
(1.00) 		0.138
(1.00)
RHOA 13 (6%) 206 0.159
(1.00) 		0.189
(1.00) 		0.871
(1.00) 		1
(1.00) 		0.623
(1.00) 		0.238
(1.00) 		0.00166
(0.382) 		0.185
(1.00) 		0.00106
(0.248) 		0.127
(1.00)
TRIM48 14 (6%) 205 0.235
(1.00) 		0.322
(1.00) 		0.0289
(1.00) 		0.164
(1.00) 		0.377
(1.00) 		0.925
(1.00) 		0.472
(1.00) 		0.28
(1.00) 		0.0931
(1.00) 		0.597
(1.00)
KRAS 25 (11%) 194 0.0145
(1.00) 		0.127
(1.00) 		0.541
(1.00) 		0.96
(1.00) 		0.262
(1.00) 		0.0511
(1.00) 		0.262
(1.00) 		0.184
(1.00) 		0.233
(1.00) 		0.947
(1.00)
SMAD4 19 (9%) 200 0.948
(1.00) 		0.963
(1.00) 		0.0592
(1.00) 		0.747
(1.00) 		0.033
(1.00) 		0.0914
(1.00) 		0.409
(1.00) 		0.618
(1.00) 		0.248
(1.00) 		0.201
(1.00)
MXRA8 10 (5%) 209 0.156
(1.00) 		0.0232
(1.00) 		0.273
(1.00) 		0.0118
(1.00) 		0.00479
(1.00) 		0.0989
(1.00) 		0.0322
(1.00) 		0.0102
(1.00) 		0.541
(1.00) 		0.125
(1.00)
IRF2 15 (7%) 204 0.158
(1.00) 		0.233
(1.00) 		0.118
(1.00) 		0.588
(1.00) 		0.059
(1.00) 		0.199
(1.00) 		0.00786
(1.00) 		0.0221
(1.00) 		0.0852
(1.00) 		0.0309
(1.00)
CDH1 18 (8%) 201 0.215
(1.00) 		0.458
(1.00) 		0.611
(1.00) 		0.443
(1.00) 		0.0481
(1.00) 		0.0529
(1.00) 		0.016
(1.00) 		0.0675
(1.00) 		0.0561
(1.00) 		0.114
(1.00)
PTEN 14 (6%) 205 0.0166
(1.00) 		0.0152
(1.00) 		0.00319
(0.711) 		0.0191
(1.00) 		0.0222
(1.00) 		0.0956
(1.00) 		0.115
(1.00) 		0.022
(1.00) 		0.207
(1.00) 		0.0121
(1.00)
FBXW7 19 (9%) 200 0.0318
(1.00) 		0.022
(1.00) 		0.00143
(0.334) 		0.00428
(0.938) 		0.00378
(0.839) 		0.942
(1.00) 		0.0467
(1.00) 		0.00412
(0.907) 		0.00402
(0.889) 		0.00596
(1.00)
B2M 8 (4%) 211 0.0175
(1.00) 		0.0232
(1.00) 		0.086
(1.00) 		0.414
(1.00) 		0.13
(1.00) 		0.683
(1.00) 		0.314
(1.00) 		0.15
(1.00) 		0.907
(1.00) 		0.125
(1.00)
PTH2 4 (2%) 215 1
(1.00) 		0.687
(1.00) 		1
(1.00) 		0.836
(1.00) 		0.336
(1.00) 		1
(1.00) 		0.467
(1.00) 		1
(1.00) 		0.821
(1.00) 		1
(1.00)
FAM46D 6 (3%) 213 0.548
(1.00) 		0.708
(1.00) 		0.744
(1.00) 		0.425
(1.00) 		0.152
(1.00) 		0.64
(1.00) 		0.878
(1.00) 		0.766
(1.00) 		1
(1.00) 		0.71
(1.00)
APC 33 (15%) 186 1
(1.00) 		0.0207
(1.00) 		0.0627
(1.00) 		0.0631
(1.00) 		0.178
(1.00) 		0.031
(1.00) 		0.00869
(1.00) 		0.0136
(1.00) 		0.0623
(1.00) 		0.00145
(0.337)
RNF43 9 (4%) 210 0.0478
(1.00) 		0.596
(1.00) 		0.576
(1.00) 		0.189
(1.00) 		0.0708
(1.00) 		0.53
(1.00) 		0.435
(1.00) 		0.182
(1.00) 		0.881
(1.00) 		0.411
(1.00)
MAP2K7 14 (6%) 205 0.0166
(1.00) 		0.0984
(1.00) 		0.822
(1.00) 		0.81
(1.00) 		0.191
(1.00) 		0.861
(1.00) 		0.308
(1.00) 		0.085
(1.00) 		0.791
(1.00) 		0.461
(1.00)
WSB2 7 (3%) 212 0.224
(1.00) 		0.131
(1.00) 		0.086
(1.00) 		0.0797
(1.00) 		0.115
(1.00) 		0.21
(1.00) 		0.0319
(1.00) 		0.00742
(1.00) 		0.252
(1.00) 		0.0666
(1.00)
TRPS1 30 (14%) 189 0.67
(1.00) 		0.0397
(1.00) 		0.106
(1.00) 		0.108
(1.00) 		0.0158
(1.00) 		0.554
(1.00) 		0.437
(1.00) 		0.414
(1.00) 		0.327
(1.00) 		0.231
(1.00)
C13ORF33 6 (3%) 213 0.749
(1.00) 		0.0165
(1.00) 		0.0147
(1.00) 		0.113
(1.00) 		0.11
(1.00) 		0.682
(1.00) 		0.589
(1.00) 		0.333
(1.00) 		0.324
(1.00) 		0.411
(1.00)
HRCT1 4 (2%) 215 0.297
(1.00) 		0.915
(1.00) 		0.348
(1.00) 		0.123
(1.00) 		0.109
(1.00) 		0.0341
(1.00) 		0.389
(1.00) 		0.332
(1.00)
IAPP 4 (2%) 215 0.377
(1.00) 		0.844
(1.00) 		0.533
(1.00) 		0.742
(1.00) 		0.214
(1.00) 		0.688
(1.00) 		0.821
(1.00)
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 5.42e-05 (Fisher's exact test), Q value = 0.013

Table S1.  Gene #2: 'PIK3CA MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 35 74
PIK3CA MUTATED 36 7 5
PIK3CA WILD-TYPE 73 28 69

Figure S1.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.83e-09 (Fisher's exact test), Q value = 4.6e-07

Table S2.  Gene #2: 'PIK3CA MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 51 44 53
PIK3CA MUTATED 19 15 4 4
PIK3CA WILD-TYPE 8 36 40 49

Figure S2.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.000478 (Fisher's exact test), Q value = 0.11

Table S3.  Gene #2: 'PIK3CA MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 38 84
PIK3CA MUTATED 7 15 23
PIK3CA WILD-TYPE 67 23 61

Figure S3.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000815 (Chi-square test), Q value = 0.19

Table S4.  Gene #2: 'PIK3CA MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 43 29 33 44
PIK3CA MUTATED 19 8 4 10 3
PIK3CA WILD-TYPE 26 35 25 23 41

Figure S4.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.05e-07 (Fisher's exact test), Q value = 0.00013

Table S5.  Gene #2: 'PIK3CA MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 97 49
PIK3CA MUTATED 5 37 2
PIK3CA WILD-TYPE 43 60 47

Figure S5.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000865 (Fisher's exact test), Q value = 0.2

Table S6.  Gene #2: 'PIK3CA MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 47 91
PIK3CA MUTATED 2 9 31
PIK3CA WILD-TYPE 36 38 60

Figure S6.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PGM5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4.28e-05 (Fisher's exact test), Q value = 0.011

Table S7.  Gene #3: 'PGM5 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 51 44 53
PGM5 MUTATED 3 12 1 0
PGM5 WILD-TYPE 24 39 43 53

Figure S7.  Get High-res Image Gene #3: 'PGM5 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'CBWD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 9.54e-05 (Fisher's exact test), Q value = 0.023

Table S8.  Gene #5: 'CBWD1 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 35 74
CBWD1 MUTATED 23 4 1
CBWD1 WILD-TYPE 86 31 73

Figure S8.  Get High-res Image Gene #5: 'CBWD1 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'CBWD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.79e-06 (Fisher's exact test), Q value = 0.00045

Table S9.  Gene #5: 'CBWD1 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 51 44 53
CBWD1 MUTATED 4 16 2 0
CBWD1 WILD-TYPE 23 35 42 53

Figure S9.  Get High-res Image Gene #5: 'CBWD1 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'CBWD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 5.26e-05 (Fisher's exact test), Q value = 0.013

Table S10.  Gene #5: 'CBWD1 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 68 67
CBWD1 MUTATED 18 2 7
CBWD1 WILD-TYPE 43 66 60

Figure S10.  Get High-res Image Gene #5: 'CBWD1 MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 9.45e-11 (Fisher's exact test), Q value = 2.4e-08

Table S11.  Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 35 74
TP53 MUTATED 24 24 49
TP53 WILD-TYPE 85 11 25

Figure S11.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.18e-05 (Fisher's exact test), Q value = 0.0079

Table S12.  Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 51 44 53
TP53 MUTATED 5 25 15 37
TP53 WILD-TYPE 22 26 29 16

Figure S12.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000382 (Chi-square test), Q value = 0.092

Table S13.  Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 43 29 33 44
TP53 MUTATED 14 12 10 18 30
TP53 WILD-TYPE 31 31 19 15 14

Figure S13.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.1e-06 (Fisher's exact test), Q value = 0.0013

Table S14.  Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 55 71
TP53 MUTATED 36 40 22
TP53 WILD-TYPE 57 15 49

Figure S14.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000325 (Fisher's exact test), Q value = 0.079

Table S15.  Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 47 91
TP53 MUTATED 27 13 43
TP53 WILD-TYPE 11 34 48

Figure S15.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 6.15e-05 (Fisher's exact test), Q value = 0.015

Table S16.  Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 35 74
ARID1A MUTATED 33 3 5
ARID1A WILD-TYPE 76 32 69

Figure S16.  Get High-res Image Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00097 (Chi-square test), Q value = 0.23

Table S17.  Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 43 29 33 44
ARID1A MUTATED 18 9 4 6 2
ARID1A WILD-TYPE 27 34 25 27 42

Figure S17.  Get High-res Image Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0046

Table S18.  Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 97 49
ARID1A MUTATED 7 31 1
ARID1A WILD-TYPE 41 66 48

Figure S18.  Get High-res Image Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.25

Table S19.  Gene #9: 'RHOA MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 52 72
RHOA MUTATED 3 8 0
RHOA WILD-TYPE 49 44 72

Figure S19.  Get High-res Image Gene #9: 'RHOA MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

'BCOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 6.67e-05 (Fisher's exact test), Q value = 0.016

Table S20.  Gene #22: 'BCOR MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 51 44 53
BCOR MUTATED 7 2 1 0
BCOR WILD-TYPE 20 49 43 53

Figure S20.  Get High-res Image Gene #22: 'BCOR MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'BCOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000453 (Fisher's exact test), Q value = 0.11

Table S21.  Gene #22: 'BCOR MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 55 71
BCOR MUTATED 14 0 2
BCOR WILD-TYPE 79 55 69

Figure S21.  Get High-res Image Gene #22: 'BCOR MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

  • Mutation data file = STAD-TP.mutsig.cluster.txt

  • Molecular subtypes file = STAD-TP.transferedmergedcluster.txt

  • Number of patients = 219

  • Number of significantly mutated genes = 26

  • Number of Molecular subtypes = 10

  • 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.

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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