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 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.

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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