Correlation between gene mutation status and molecular subtypes

Pheochromocytoma and Paraganglioma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

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 (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1K35SKD

Overview

Introduction

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

Summary

Testing the association between mutation status of 9 genes and 8 molecular subtypes across 178 patients, 18 significant findings detected with P value < 0.05 and Q value < 0.25.

HRAS mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
EPAS1 mutation correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
NF1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 9 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 18 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	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	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
HRAS	18 (10%)	160	2e-05 (0.0014)	6e-05 (0.00402)	1e-05 (0.00071)	2e-05 (0.0014)	6e-05 (0.00402)	0.00019 (0.0116)	0.00012 (0.00768)	0.00041 (0.0246)
EPAS1	8 (4%)	170	0.0109 (0.48)	0.00676 (0.324)	0.00133 (0.0771)	0.00166 (0.0913)	0.00162 (0.0907)	0.0165 (0.709)	0.00018 (0.0112)	0.00191 (0.103)
NF1	15 (8%)	163	0.00013 (0.00819)	0.00057 (0.0336)	0.00942 (0.433)	5e-05 (0.0034)	0.00011 (0.00715)	0.00637 (0.312)	0.00991 (0.446)	0.00134 (0.0771)
RET	6 (3%)	172	0.00522 (0.277)	0.486 (1.00)	0.0898 (1.00)	0.105 (1.00)	0.436 (1.00)	0.0681 (1.00)	0.258 (1.00)	0.184 (1.00)
CSDE1	4 (2%)	174	0.285 (1.00)	0.583 (1.00)	0.49 (1.00)	0.00541 (0.281)	0.35 (1.00)	0.00578 (0.295)	0.00744 (0.35)	0.00601 (0.3)
GPR128	4 (2%)	174	1 (1.00)	0.101 (1.00)	0.891 (1.00)	0.888 (1.00)	0.543 (1.00)	0.774 (1.00)	0.53 (1.00)	0.559 (1.00)
AMMECR1	3 (2%)	175	0.79 (1.00)	1 (1.00)	0.244 (1.00)	0.628 (1.00)	0.796 (1.00)	1 (1.00)	0.594 (1.00)	0.793 (1.00)
SHROOM4	3 (2%)	175		1 (1.00)	0.467 (1.00)	0.541 (1.00)	1 (1.00)	0.679 (1.00)	0.724 (1.00)	0.638 (1.00)
FAM83D	3 (2%)	175	0.344 (1.00)	0.334 (1.00)	0.409 (1.00)	0.463 (1.00)	0.0576 (1.00)	0.815 (1.00)	0.228 (1.00)	0.439 (1.00)

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0014

Table S1. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	63	38
HRAS MUTATED	14	0	1
HRAS WILD-TYPE	46	63	37

Figure S1. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.004

Table S2. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	85	49
HRAS MUTATED	0	17	1
HRAS WILD-TYPE	44	68	48

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

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00071

Table S3. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	69	49	21
HRAS MUTATED	0	18	0	0
HRAS WILD-TYPE	39	51	49	21

Figure S3. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0014

Table S4. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	71	48	21
HRAS MUTATED	0	18	0	0
HRAS WILD-TYPE	38	53	48	21

Figure S4. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.004

Table S5. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	65	39
HRAS MUTATED	1	15	2
HRAS WILD-TYPE	73	50	37

Figure S5. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.012

Table S6. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	59	18	25
HRAS MUTATED	1	14	1	2
HRAS WILD-TYPE	75	45	17	23

Figure S6. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0077

Table S7. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	64	12	41	24
HRAS MUTATED	1	15	2	0	0
HRAS WILD-TYPE	35	49	10	41	24

Figure S7. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.025

Table S8. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	80	60	18	19
HRAS MUTATED	16	0	1	1
HRAS WILD-TYPE	64	60	17	18

Figure S8. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.48

Table S9. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	63	38
EPAS1 MUTATED	0	7	1
EPAS1 WILD-TYPE	60	56	37

Figure S9. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'EPAS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00676 (Fisher's exact test), Q value = 0.32

Table S10. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	85	49
EPAS1 MUTATED	4	0	4
EPAS1 WILD-TYPE	40	85	45

Figure S10. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.077

Table S11. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	69	49	21
EPAS1 MUTATED	1	0	7	0
EPAS1 WILD-TYPE	38	69	42	21

Figure S11. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.091

Table S12. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	71	48	21
EPAS1 MUTATED	1	0	7	0
EPAS1 WILD-TYPE	37	71	41	21

Figure S12. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00162 (Fisher's exact test), Q value = 0.091

Table S13. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	65	39
EPAS1 MUTATED	8	0	0
EPAS1 WILD-TYPE	66	65	39

Figure S13. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.71

Table S14. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	59	18	25
EPAS1 MUTATED	8	0	0	0
EPAS1 WILD-TYPE	68	59	18	25

Figure S14. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.011

Table S15. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	64	12	41	24
EPAS1 MUTATED	0	0	1	7	0
EPAS1 WILD-TYPE	36	64	11	34	24

Figure S15. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00191 (Fisher's exact test), Q value = 0.1

Table S16. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	80	60	18	19
EPAS1 MUTATED	0	8	0	0
EPAS1 WILD-TYPE	80	52	18	19

Figure S16. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0082

Table S17. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	63	38
NF1 MUTATED	3	1	10
NF1 WILD-TYPE	57	62	28

Figure S17. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.034

Table S18. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	85	49
NF1 MUTATED	0	14	1
NF1 WILD-TYPE	44	71	48

Figure S18. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00942 (Fisher's exact test), Q value = 0.43

Table S19. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	69	49	21
NF1 MUTATED	3	11	0	1
NF1 WILD-TYPE	36	58	49	20

Figure S19. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0034

Table S20. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	71	48	21
NF1 MUTATED	0	14	0	1
NF1 WILD-TYPE	38	57	48	20

Figure S20. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0071

Table S21. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	65	39
NF1 MUTATED	1	13	1
NF1 WILD-TYPE	73	52	38

Figure S21. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00637 (Fisher's exact test), Q value = 0.31

Table S22. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	59	18	25
NF1 MUTATED	2	11	0	2
NF1 WILD-TYPE	74	48	18	23

Figure S22. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00991 (Fisher's exact test), Q value = 0.45

Table S23. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	64	12	41	24
NF1 MUTATED	3	10	2	0	0
NF1 WILD-TYPE	33	54	10	41	24

Figure S23. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00134 (Fisher's exact test), Q value = 0.077

Table S24. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	80	60	18	19
NF1 MUTATED	13	0	0	2
NF1 WILD-TYPE	67	60	18	17

Figure S24. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00522 (Fisher's exact test), Q value = 0.28

Table S25. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	63	38
RET MUTATED	6	0	0
RET WILD-TYPE	54	63	38

Figure S25. Get High-res Image Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.486 (Fisher's exact test), Q value = 1

Table S26. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	85	49
RET MUTATED	0	4	2
RET WILD-TYPE	44	81	47

'RET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0898 (Fisher's exact test), Q value = 1

Table S27. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	69	49	21
RET MUTATED	0	5	0	1
RET WILD-TYPE	39	64	49	20

'RET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.105 (Fisher's exact test), Q value = 1

Table S28. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	71	48	21
RET MUTATED	0	5	0	1
RET WILD-TYPE	38	66	48	20

'RET MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.436 (Fisher's exact test), Q value = 1

Table S29. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	65	39
RET MUTATED	1	3	2
RET WILD-TYPE	73	62	37

'RET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0681 (Fisher's exact test), Q value = 1

Table S30. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	59	18	25
RET MUTATED	0	4	1	1
RET WILD-TYPE	76	55	17	24

'RET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 1

Table S31. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	64	12	41	24
RET MUTATED	1	4	1	0	0
RET WILD-TYPE	35	60	11	41	24

'RET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.184 (Fisher's exact test), Q value = 1

Table S32. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	80	60	18	19
RET MUTATED	4	0	1	1
RET WILD-TYPE	76	60	17	18

'CSDE1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.285 (Fisher's exact test), Q value = 1

Table S33. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	63	38
CSDE1 MUTATED	0	3	1
CSDE1 WILD-TYPE	60	60	37

'CSDE1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.583 (Fisher's exact test), Q value = 1

Table S34. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	85	49
CSDE1 MUTATED	1	3	0
CSDE1 WILD-TYPE	43	82	49

'CSDE1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 1

Table S35. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	69	49	21
CSDE1 MUTATED	1	3	0	0
CSDE1 WILD-TYPE	38	66	49	21

'CSDE1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00541 (Fisher's exact test), Q value = 0.28

Table S36. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	71	48	21
CSDE1 MUTATED	4	0	0	0
CSDE1 WILD-TYPE	34	71	48	21

Figure S26. Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CSDE1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 1

Table S37. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	65	39
CSDE1 MUTATED	1	3	0
CSDE1 WILD-TYPE	73	62	39

'CSDE1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00578 (Fisher's exact test), Q value = 0.29

Table S38. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	59	18	25
CSDE1 MUTATED	1	0	3	0
CSDE1 WILD-TYPE	75	59	15	25

Figure S27. Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'CSDE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00744 (Fisher's exact test), Q value = 0.35

Table S39. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	64	12	41	24
CSDE1 MUTATED	4	0	0	0	0
CSDE1 WILD-TYPE	32	64	12	41	24

Figure S28. Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'CSDE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00601 (Fisher's exact test), Q value = 0.3

Table S40. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	80	60	18	19
CSDE1 MUTATED	1	0	3	0
CSDE1 WILD-TYPE	79	60	15	19

Figure S29. Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GPR128 MUTATION STATUS' versus 'CN_CNMF'

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

Table S41. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	63	38
GPR128 MUTATED	1	1	1
GPR128 WILD-TYPE	59	62	37

'GPR128 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 1

Table S42. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	85	49
GPR128 MUTATED	3	1	0
GPR128 WILD-TYPE	41	84	49

'GPR128 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.891 (Fisher's exact test), Q value = 1

Table S43. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	69	49	21
GPR128 MUTATED	1	1	2	0
GPR128 WILD-TYPE	38	68	47	21

'GPR128 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.888 (Fisher's exact test), Q value = 1

Table S44. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	71	48	21
GPR128 MUTATED	1	1	2	0
GPR128 WILD-TYPE	37	70	46	21

'GPR128 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.543 (Fisher's exact test), Q value = 1

Table S45. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	65	39
GPR128 MUTATED	3	1	0
GPR128 WILD-TYPE	71	64	39

'GPR128 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.774 (Fisher's exact test), Q value = 1

Table S46. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	59	18	25
GPR128 MUTATED	3	1	0	0
GPR128 WILD-TYPE	73	58	18	25

'GPR128 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.53 (Fisher's exact test), Q value = 1

Table S47. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	64	12	41	24
GPR128 MUTATED	0	1	0	2	1
GPR128 WILD-TYPE	36	63	12	39	23

'GPR128 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.559 (Fisher's exact test), Q value = 1

Table S48. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	80	60	18	19
GPR128 MUTATED	1	3	0	0
GPR128 WILD-TYPE	79	57	18	19

'AMMECR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.79 (Fisher's exact test), Q value = 1

Table S49. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	63	38
AMMECR1 MUTATED	1	2	0
AMMECR1 WILD-TYPE	59	61	38

'AMMECR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S50. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	85	49
AMMECR1 MUTATED	1	1	1
AMMECR1 WILD-TYPE	43	84	48

'AMMECR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 1

Table S51. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	69	49	21
AMMECR1 MUTATED	1	0	2	0
AMMECR1 WILD-TYPE	38	69	47	21

'AMMECR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.628 (Fisher's exact test), Q value = 1

Table S52. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	71	48	21
AMMECR1 MUTATED	0	1	2	0
AMMECR1 WILD-TYPE	38	70	46	21

'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S53. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	65	39
AMMECR1 MUTATED	2	1	0
AMMECR1 WILD-TYPE	72	64	39

'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S54. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	59	18	25
AMMECR1 MUTATED	2	1	0	0
AMMECR1 WILD-TYPE	74	58	18	25

'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.594 (Fisher's exact test), Q value = 1

Table S55. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	64	12	41	24
AMMECR1 MUTATED	0	1	0	2	0
AMMECR1 WILD-TYPE	36	63	12	39	24

'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S56. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	80	60	18	19
AMMECR1 MUTATED	1	2	0	0
AMMECR1 WILD-TYPE	79	58	18	19

'SHROOM4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S57. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	85	49
SHROOM4 MUTATED	1	1	1
SHROOM4 WILD-TYPE	43	84	48

'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 1

Table S58. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	69	49	21
SHROOM4 MUTATED	1	1	0	1
SHROOM4 WILD-TYPE	38	68	49	20

'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S59. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	71	48	21
SHROOM4 MUTATED	0	1	1	1
SHROOM4 WILD-TYPE	38	70	47	20

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S60. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	65	39
SHROOM4 MUTATED	1	1	1
SHROOM4 WILD-TYPE	73	64	38

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 1

Table S61. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	59	18	25
SHROOM4 MUTATED	1	1	0	1
SHROOM4 WILD-TYPE	75	58	18	24

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S62. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	64	12	41	24
SHROOM4 MUTATED	0	1	0	1	1
SHROOM4 WILD-TYPE	36	63	12	40	23

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.638 (Fisher's exact test), Q value = 1

Table S63. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	80	60	18	19
SHROOM4 MUTATED	1	1	0	1
SHROOM4 WILD-TYPE	79	59	18	18

'FAM83D MUTATION STATUS' versus 'CN_CNMF'

P value = 0.344 (Fisher's exact test), Q value = 1

Table S64. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	63	38
FAM83D MUTATED	2	0	1
FAM83D WILD-TYPE	58	63	37

'FAM83D MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.334 (Fisher's exact test), Q value = 1

Table S65. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	85	49
FAM83D MUTATED	0	3	0
FAM83D WILD-TYPE	44	82	49

'FAM83D MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.409 (Fisher's exact test), Q value = 1

Table S66. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	69	49	21
FAM83D MUTATED	0	3	0	0
FAM83D WILD-TYPE	39	66	49	21

'FAM83D MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.463 (Fisher's exact test), Q value = 1

Table S67. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	71	48	21
FAM83D MUTATED	0	3	0	0
FAM83D WILD-TYPE	38	68	48	21

'FAM83D MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0576 (Fisher's exact test), Q value = 1

Table S68. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	65	39
FAM83D MUTATED	0	3	0
FAM83D WILD-TYPE	74	62	39

'FAM83D MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.815 (Fisher's exact test), Q value = 1

Table S69. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	59	18	25
FAM83D MUTATED	1	2	0	0
FAM83D WILD-TYPE	75	57	18	25

'FAM83D MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.228 (Fisher's exact test), Q value = 1

Table S70. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	64	12	41	24
FAM83D MUTATED	0	2	1	0	0
FAM83D WILD-TYPE	36	62	11	41	24

'FAM83D MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.439 (Fisher's exact test), Q value = 1

Table S71. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	80	60	18	19
FAM83D MUTATED	3	0	0	0
FAM83D WILD-TYPE	77	60	18	19

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = PCPG-TP.transferedmergedcluster.txt
Number of patients = 178
Number of significantly mutated genes = 9
Number of Molecular subtypes = 8
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.

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] 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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