Correlation between gene mutation status and molecular subtypes

Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)

15 January 2014 | analyses__2014_01_15

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/C10R9MW5

Overview

Introduction

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

Summary

Testing the association between mutation status of 7 genes and 6 molecular subtypes across 196 patients, 16 significant findings detected with P value < 0.05 and Q value < 0.25.

DNMT3A mutation correlated to 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
FLT3 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
IDH2 mutation correlated to 'METHLYATION_CNMF'.
IDH1 mutation correlated to 'METHLYATION_CNMF'.
NPM1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 7 genes and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 16 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nMutated (%)	nWild-Type	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
NPM1	54 (28%)	142	4.59e-06 (0.000156)	3.26e-20 (1.34e-18)	3.08e-13 (1.2e-11)	0.00649 (0.175)	1.59e-13 (6.36e-12)	3.26e-22 (1.37e-20)
FLT3	56 (29%)	140	0.000153 (0.00474)	2.48e-05 (0.000819)	2.2e-07 (8.36e-06)	0.0209 (0.523)	0.0005 (0.015)	4.14e-05 (0.00132)
DNMT3A	51 (26%)	145	0.511 (1.00)	4e-07 (1.48e-05)	0.0118 (0.308)	0.195 (1.00)	0.000888 (0.0258)	4.26e-06 (0.000149)
IDH2	20 (10%)	176	0.109 (1.00)	1.59e-06 (5.74e-05)	0.733 (1.00)	1 (1.00)	0.739 (1.00)	0.61 (1.00)
IDH1	19 (10%)	177	0.321 (1.00)	0.00563 (0.158)	0.433 (1.00)	0.268 (1.00)	0.281 (1.00)	0.436 (1.00)
U2AF1	8 (4%)	188	1 (1.00)	0.128 (1.00)	0.232 (1.00)	0.426 (1.00)	0.0716 (1.00)	0.234 (1.00)
NRAS	15 (8%)	181	0.297 (1.00)	0.892 (1.00)	0.645 (1.00)	0.539 (1.00)	0.825 (1.00)	0.756 (1.00)

'DNMT3A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.511 (Fisher's exact test), Q value = 1

Table S1. Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	14	27	3
DNMT3A MUTATED	38	4	4	1
DNMT3A WILD-TYPE	105	10	23	2

'DNMT3A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4e-07 (Chi-square test), Q value = 1.5e-05

Table S2. Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	44	65	14	20
DNMT3A MUTATED	25	1	19	1	3
DNMT3A WILD-TYPE	22	43	46	13	17

Figure S1. Get High-res Image Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.31

Table S3. Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	73	52	45
DNMT3A MUTATED	11	20	12
DNMT3A WILD-TYPE	62	32	33

Figure S2. Get High-res Image Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 1

Table S4. Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	57	113
DNMT3A MUTATED	18	25
DNMT3A WILD-TYPE	39	88

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000888 (Fisher's exact test), Q value = 0.026

Table S5. Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	38	42	46
DNMT3A MUTATED	24	4	5	13
DNMT3A WILD-TYPE	34	34	37	33

Figure S3. Get High-res Image Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.26e-06 (Fisher's exact test), Q value = 0.00015

Table S6. Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	80	68
DNMT3A MUTATED	2	34	10
DNMT3A WILD-TYPE	34	46	58

Figure S4. Get High-res Image Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'U2AF1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S7. Gene #2: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	14	27	3
U2AF1 MUTATED	5	0	1	0
U2AF1 WILD-TYPE	138	14	26	3

'U2AF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.128 (Chi-square test), Q value = 1

Table S8. Gene #2: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	44	65	14	20
U2AF1 MUTATED	1	0	6	0	1
U2AF1 WILD-TYPE	46	44	59	14	19

'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 1

Table S9. Gene #2: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	73	52	45
U2AF1 MUTATED	5	2	0
U2AF1 WILD-TYPE	68	50	45

'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.426 (Fisher's exact test), Q value = 1

Table S10. Gene #2: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	57	113
U2AF1 MUTATED	1	6
U2AF1 WILD-TYPE	56	107

'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0716 (Fisher's exact test), Q value = 1

Table S11. Gene #2: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	38	42	46
U2AF1 MUTATED	1	2	4	0
U2AF1 WILD-TYPE	57	36	38	46

'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.234 (Fisher's exact test), Q value = 1

Table S12. Gene #2: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	80	68
U2AF1 MUTATED	2	1	4
U2AF1 WILD-TYPE	34	79	64

'FLT3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000153 (Fisher's exact test), Q value = 0.0047

Table S13. Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	14	27	3
FLT3 MUTATED	51	3	0	0
FLT3 WILD-TYPE	92	11	27	3

Figure S5. Get High-res Image Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FLT3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.48e-05 (Chi-square test), Q value = 0.00082

Table S14. Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	44	65	14	20
FLT3 MUTATED	26	12	8	2	7
FLT3 WILD-TYPE	21	32	57	12	13

Figure S6. Get High-res Image Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FLT3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2.2e-07 (Fisher's exact test), Q value = 8.4e-06

Table S15. Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	73	52	45
FLT3 MUTATED	6	20	23
FLT3 WILD-TYPE	67	32	22

Figure S7. Get High-res Image Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'FLT3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.52

Table S16. Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	57	113
FLT3 MUTATED	23	26
FLT3 WILD-TYPE	34	87

Figure S8. Get High-res Image Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'FLT3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.015

Table S17. Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	38	42	46
FLT3 MUTATED	25	4	7	18
FLT3 WILD-TYPE	33	34	35	28

Figure S9. Get High-res Image Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'FLT3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.14e-05 (Fisher's exact test), Q value = 0.0013

Table S18. Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	80	68
FLT3 MUTATED	4	37	13
FLT3 WILD-TYPE	32	43	55

Figure S10. Get High-res Image Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'IDH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 1

Table S19. Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	14	27	3
IDH2 MUTATED	14	4	1	0
IDH2 WILD-TYPE	129	10	26	3

'IDH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.59e-06 (Chi-square test), Q value = 5.7e-05

Table S20. Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	44	65	14	20
IDH2 MUTATED	0	0	11	6	1
IDH2 WILD-TYPE	47	44	54	8	19

Figure S11. Get High-res Image Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.733 (Fisher's exact test), Q value = 1

Table S21. Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	73	52	45
IDH2 MUTATED	8	6	3
IDH2 WILD-TYPE	65	46	42

'IDH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S22. Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	57	113
IDH2 MUTATED	6	11
IDH2 WILD-TYPE	51	102

'IDH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.739 (Fisher's exact test), Q value = 1

Table S23. Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	38	42	46
IDH2 MUTATED	5	2	5	5
IDH2 WILD-TYPE	53	36	37	41

'IDH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.61 (Fisher's exact test), Q value = 1

Table S24. Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	80	68
IDH2 MUTATED	2	7	8
IDH2 WILD-TYPE	34	73	60

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 1

Table S25. Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	14	27	3
IDH1 MUTATED	15	1	1	1
IDH1 WILD-TYPE	128	13	26	2

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00563 (Chi-square test), Q value = 0.16

Table S26. Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	44	65	14	20
IDH1 MUTATED	5	0	10	4	0
IDH1 WILD-TYPE	42	44	55	10	20

Figure S12. Get High-res Image Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.433 (Fisher's exact test), Q value = 1

Table S27. Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	73	52	45
IDH1 MUTATED	7	3	6
IDH1 WILD-TYPE	66	49	39

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.268 (Fisher's exact test), Q value = 1

Table S28. Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	57	113
IDH1 MUTATED	3	13
IDH1 WILD-TYPE	54	100

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.281 (Fisher's exact test), Q value = 1

Table S29. Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	38	42	46
IDH1 MUTATED	5	4	2	8
IDH1 WILD-TYPE	53	34	40	38

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S30. Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	80	68
IDH1 MUTATED	3	11	5
IDH1 WILD-TYPE	33	69	63

'NPM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 4.59e-06 (Fisher's exact test), Q value = 0.00016

Table S31. Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	14	27	3
NPM1 MUTATED	52	0	0	0
NPM1 WILD-TYPE	91	14	27	3

Figure S13. Get High-res Image Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NPM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.26e-20 (Chi-square test), Q value = 1.3e-18

Table S32. Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	44	65	14	20
NPM1 MUTATED	36	0	4	9	4
NPM1 WILD-TYPE	11	44	61	5	16

Figure S14. Get High-res Image Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NPM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3.08e-13 (Fisher's exact test), Q value = 1.2e-11

Table S33. Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	73	52	45
NPM1 MUTATED	1	22	25
NPM1 WILD-TYPE	72	30	20

Figure S15. Get High-res Image Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'NPM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00649 (Fisher's exact test), Q value = 0.18

Table S34. Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	57	113
NPM1 MUTATED	24	24
NPM1 WILD-TYPE	33	89

Figure S16. Get High-res Image Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'NPM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.59e-13 (Fisher's exact test), Q value = 6.4e-12

Table S35. Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	38	42	46
NPM1 MUTATED	37	2	1	12
NPM1 WILD-TYPE	21	36	41	34

Figure S17. Get High-res Image Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'NPM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.26e-22 (Fisher's exact test), Q value = 1.4e-20

Table S36. Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	80	68
NPM1 MUTATED	0	51	1
NPM1 WILD-TYPE	36	29	67

Figure S18. Get High-res Image Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 1

Table S37. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	143	14	27	3
NRAS MUTATED	10	1	3	1
NRAS WILD-TYPE	133	13	24	2

'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.892 (Chi-square test), Q value = 1

Table S38. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	44	65	14	20
NRAS MUTATED	4	3	5	2	1
NRAS WILD-TYPE	43	41	60	12	19

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S39. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	73	52	45
NRAS MUTATED	5	5	2
NRAS WILD-TYPE	68	47	43

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.539 (Fisher's exact test), Q value = 1

Table S40. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	57	113
NRAS MUTATED	5	7
NRAS WILD-TYPE	52	106

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.825 (Fisher's exact test), Q value = 1

Table S41. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	38	42	46
NRAS MUTATED	5	3	4	2
NRAS WILD-TYPE	53	35	38	44

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.756 (Fisher's exact test), Q value = 1

Table S42. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	80	68
NRAS MUTATED	3	7	4
NRAS WILD-TYPE	33	73	64

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = LAML-TB.transferedmergedcluster.txt
Number of patients = 196
Number of significantly mutated genes = 7
Number of Molecular subtypes = 6
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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