Correlation between gene mutation status and molecular subtypes

Pheochromocytoma and Paraganglioma (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

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 (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1H13186

Overview

Introduction

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

Summary

Testing the association between mutation status of 8 genes and 10 molecular subtypes across 178 patients, 27 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 8 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, 27 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	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	3e-05 (8e-04)	6e-05 (0.00112)	0.157 (0.38)	0.00111 (0.00634)	1e-05 (4e-04)	1e-05 (4e-04)	7e-05 (0.00112)	0.00021 (0.00153)	0.00014 (0.00144)	0.00032 (0.00213)
NF1	15 (8%)	163	0.00013 (0.00144)	0.0008 (0.00492)	0.00747 (0.026)	0.0867 (0.239)	0.00973 (0.0313)	0.00015 (0.00144)	0.00018 (0.00144)	0.00601 (0.0229)	0.00978 (0.0313)	0.00123 (0.00656)
EPAS1	8 (4%)	170	0.0109 (0.0334)	0.00633 (0.023)	0.357 (0.696)	0.356 (0.696)	0.00158 (0.00742)	0.00162 (0.00742)	0.00206 (0.00867)	0.016 (0.0474)	0.00018 (0.00144)	0.00167 (0.00742)
RET	6 (3%)	172	0.00484 (0.0194)	0.483 (0.84)	0.428 (0.809)	0.326 (0.686)	0.0902 (0.24)	0.105 (0.263)	0.435 (0.809)	0.0673 (0.192)	0.258 (0.573)	0.183 (0.431)
NUDT11	5 (3%)	173	0.736 (0.978)	0.716 (0.978)	0.786 (0.978)	1 (1.00)	0.347 (0.696)	0.722 (0.978)	0.449 (0.817)	0.284 (0.615)	0.948 (1.00)	0.665 (0.966)
SHROOM4	3 (2%)	175		1 (1.00)			0.468 (0.832)	0.542 (0.877)	1 (1.00)	0.676 (0.966)	0.723 (0.978)	0.635 (0.941)
AMMECR1	3 (2%)	175	0.789 (0.978)	1 (1.00)	0.548 (0.877)	1 (1.00)	0.242 (0.554)	0.627 (0.941)	0.794 (0.978)	1 (1.00)	0.594 (0.913)	0.792 (0.978)
GPR128	4 (2%)	174	1 (1.00)	0.1 (0.259)			0.889 (1.00)	0.888 (1.00)	0.541 (0.877)	0.775 (0.978)	0.528 (0.877)	0.559 (0.877)

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 8e-04

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 = 0.0011

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 'RPPA_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.38

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	21	23	18
HRAS MUTATED	3	2	5	0
HRAS WILD-TYPE	14	19	18	18

'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.0063

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	28
HRAS MUTATED	1	7	2
HRAS WILD-TYPE	32	11	26

Figure S3. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4e-04

Table S5. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: '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 S4. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4e-04

Table S6. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: '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 S5. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0011

Table S7. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: '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 S6. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0015

Table S8. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: '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 S7. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0014

Table S9. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: '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 S8. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0021

Table S10. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: '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 S9. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0014

Table S11. Gene #2: '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 S10. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0049

Table S12. Gene #2: '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 S11. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00747 (Fisher's exact test), Q value = 0.026

Table S13. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	21	23	18
NF1 MUTATED	3	0	6	0
NF1 WILD-TYPE	14	21	17	18

Figure S12. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0867 (Fisher's exact test), Q value = 0.24

Table S14. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	28
NF1 MUTATED	1	4	4
NF1 WILD-TYPE	32	14	24

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00973 (Fisher's exact test), Q value = 0.031

Table S15. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: '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 S13. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0014

Table S16. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: '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 S14. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0014

Table S17. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: '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 S15. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00601 (Fisher's exact test), Q value = 0.023

Table S18. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: '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 S16. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00978 (Fisher's exact test), Q value = 0.031

Table S19. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: '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 S17. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00123 (Fisher's exact test), Q value = 0.0066

Table S20. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: '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 S18. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.033

Table S21. Gene #3: '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 S19. Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'EPAS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00633 (Fisher's exact test), Q value = 0.023

Table S22. Gene #3: '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 S20. Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPAS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 0.7

Table S23. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	21	23	18
EPAS1 MUTATED	1	3	1	0
EPAS1 WILD-TYPE	16	18	22	18

'EPAS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.356 (Fisher's exact test), Q value = 0.7

Table S24. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	28
EPAS1 MUTATED	2	0	3
EPAS1 WILD-TYPE	31	18	25

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.0074

Table S25. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: '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 S21. Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00162 (Fisher's exact test), Q value = 0.0074

Table S26. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #6: '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 S22. Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.0087

Table S27. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: '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 S23. Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.047

Table S28. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #8: '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 S24. Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0014

Table S29. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #9: '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 S25. Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00167 (Fisher's exact test), Q value = 0.0074

Table S30. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #10: '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 S26. Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NUDT11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.736 (Fisher's exact test), Q value = 0.98

Table S31. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	63	38
NUDT11 MUTATED	1	2	2
NUDT11 WILD-TYPE	59	61	36

'NUDT11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.716 (Fisher's exact test), Q value = 0.98

Table S32. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	85	49
NUDT11 MUTATED	2	2	1
NUDT11 WILD-TYPE	42	83	48

'NUDT11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.786 (Fisher's exact test), Q value = 0.98

Table S33. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	21	23	18
NUDT11 MUTATED	1	0	1	1
NUDT11 WILD-TYPE	16	21	22	17

'NUDT11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S34. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	28
NUDT11 MUTATED	1	1	1
NUDT11 WILD-TYPE	32	17	27

'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.347 (Fisher's exact test), Q value = 0.7

Table S35. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	69	49	21
NUDT11 MUTATED	2	3	0	0
NUDT11 WILD-TYPE	37	66	49	21

'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.722 (Fisher's exact test), Q value = 0.98

Table S36. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	71	48	21
NUDT11 MUTATED	0	3	2	0
NUDT11 WILD-TYPE	38	68	46	21

'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 0.82

Table S37. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	65	39
NUDT11 MUTATED	2	3	0
NUDT11 WILD-TYPE	72	62	39

'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.284 (Fisher's exact test), Q value = 0.61

Table S38. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	76	59	18	25
NUDT11 MUTATED	1	4	0	0
NUDT11 WILD-TYPE	75	55	18	25

'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.948 (Fisher's exact test), Q value = 1

Table S39. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	64	12	41	24
NUDT11 MUTATED	1	3	0	1	0
NUDT11 WILD-TYPE	35	61	12	40	24

'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.665 (Fisher's exact test), Q value = 0.97

Table S40. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	80	60	18	19
NUDT11 MUTATED	4	1	0	0
NUDT11 WILD-TYPE	76	59	18	19

'RET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00484 (Fisher's exact test), Q value = 0.019

Table S41. Gene #5: '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 S27. Get High-res Image Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 0.84

Table S42. Gene #5: '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 'RPPA_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 0.81

Table S43. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	21	23	18
RET MUTATED	1	0	2	0
RET WILD-TYPE	16	21	21	18

'RET MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 0.69

Table S44. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	28
RET MUTATED	0	1	2
RET WILD-TYPE	33	17	26

'RET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0902 (Fisher's exact test), Q value = 0.24

Table S45. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.26

Table S46. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.435 (Fisher's exact test), Q value = 0.81

Table S47. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.0673 (Fisher's exact test), Q value = 0.19

Table S48. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.57

Table S49. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.183 (Fisher's exact test), Q value = 0.43

Table S50. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #10: '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

'SHROOM4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S51. Gene #6: '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 = 0.468 (Fisher's exact test), Q value = 0.83

Table S52. Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.542 (Fisher's exact test), Q value = 0.88

Table S53. Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #6: '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 S54. Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.676 (Fisher's exact test), Q value = 0.97

Table S55. Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.723 (Fisher's exact test), Q value = 0.98

Table S56. Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.635 (Fisher's exact test), Q value = 0.94

Table S57. Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #10: '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

'AMMECR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.789 (Fisher's exact test), Q value = 0.98

Table S58. 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 S59. 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 'RPPA_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 0.88

Table S60. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	21	23	18
AMMECR1 MUTATED	0	2	1	0
AMMECR1 WILD-TYPE	17	19	22	18

'AMMECR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S61. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	28
AMMECR1 MUTATED	1	1	1
AMMECR1 WILD-TYPE	32	17	27

'AMMECR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 0.55

Table S62. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.627 (Fisher's exact test), Q value = 0.94

Table S63. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.794 (Fisher's exact test), Q value = 0.98

Table S64. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #7: '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 S65. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.91

Table S66. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.792 (Fisher's exact test), Q value = 0.98

Table S67. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #10: '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

'GPR128 MUTATION STATUS' versus 'CN_CNMF'

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

Table S68. Gene #8: '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 = 0.1 (Fisher's exact test), Q value = 0.26

Table S69. Gene #8: '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 = 0.889 (Fisher's exact test), Q value = 1

Table S70. Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #5: '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 S71. Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.541 (Fisher's exact test), Q value = 0.88

Table S72. Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.775 (Fisher's exact test), Q value = 0.98

Table S73. Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.528 (Fisher's exact test), Q value = 0.88

Table S74. Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.88

Table S75. Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #10: '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

Methods & Data

Input

Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/19897197/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PCPG-TP/20140092/PCPG-TP.transferedmergedcluster.txt
Number of patients = 178
Number of significantly mutated genes = 8
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

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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