Correlation between gene mutation status and molecular subtypes

Stomach Adenocarcinoma (Primary solid tumor)

23 September 2013 | analyses__2013_09_23

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1WD3XZ4

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.

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.

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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