Correlation between gene mutation status and molecular subtypes

Rectum Adenocarcinoma (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/C1RB73HZ

Overview

Introduction

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

Summary

Testing the association between mutation status of 12 genes and 9 molecular subtypes across 69 patients, 2 significant findings detected with P value < 0.05 and Q value < 0.25.

TP53 mutation correlated to 'MRNA_CNMF'.
KRAS mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 12 genes and 9 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 2 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ 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
TP53	44 (64%)	25	0.00014 (0.014)	0.0148 (1.00)	0.127 (1.00)	0.161 (1.00)	0.843 (1.00)	0.488 (1.00)	0.654 (1.00)	1 (1.00)	0.146 (1.00)
KRAS	38 (55%)	31	0.248 (1.00)	0.00762 (0.739)	0.00722 (0.708)	0.831 (1.00)	0.854 (1.00)	0.0459 (1.00)	0.00013 (0.0131)	0.292 (1.00)	0.00615 (0.609)
APC	56 (81%)	13	0.923 (1.00)	0.915 (1.00)	0.498 (1.00)	0.361 (1.00)	0.381 (1.00)	0.243 (1.00)	1 (1.00)	0.458 (1.00)	0.627 (1.00)
SMAD4	8 (12%)	61	0.079 (1.00)	0.779 (1.00)	1 (1.00)	0.152 (1.00)	0.0556 (1.00)	0.188 (1.00)	0.229 (1.00)	0.309 (1.00)	0.264 (1.00)
FBXW7	9 (13%)	60	0.192 (1.00)	0.41 (1.00)	0.41 (1.00)	0.69 (1.00)	0.632 (1.00)	1 (1.00)	0.117 (1.00)	0.804 (1.00)	0.576 (1.00)
NRAS	5 (7%)	64	1 (1.00)	0.841 (1.00)	0.737 (1.00)			1 (1.00)	1 (1.00)	0.0973 (1.00)	1 (1.00)
ARID1A	5 (7%)	64	0.364 (1.00)	0.392 (1.00)	0.917 (1.00)	0.173 (1.00)	0.531 (1.00)	1 (1.00)	1 (1.00)	0.314 (1.00)	0.258 (1.00)
RBM10	4 (6%)	65	1 (1.00)	0.788 (1.00)	1 (1.00)	1 (1.00)	0.779 (1.00)	0.0161 (1.00)	0.0438 (1.00)	0.532 (1.00)	0.567 (1.00)
TCF7L2	7 (10%)	62	0.782 (1.00)	0.208 (1.00)	1 (1.00)	0.153 (1.00)	0.292 (1.00)	1 (1.00)	0.305 (1.00)	1 (1.00)	0.687 (1.00)
ERBB2	4 (6%)	65	1 (1.00)	0.875 (1.00)	1 (1.00)	0.673 (1.00)	0.409 (1.00)	0.0324 (1.00)	0.0331 (1.00)	1 (1.00)	1 (1.00)
KIAA1804	9 (13%)	60	0.51 (1.00)	0.835 (1.00)	0.0305 (1.00)	1 (1.00)	0.596 (1.00)	1 (1.00)	0.761 (1.00)	0.806 (1.00)	0.576 (1.00)
CCDC88C	3 (4%)	66						1 (1.00)	0.596 (1.00)	0.432 (1.00)	0.463 (1.00)

'APC MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.923 (Fisher's exact test), Q value = 1

Table S1. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	21	19
APC MUTATED	19	16	16
APC WILD-TYPE	5	5	3

'APC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S2. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	6	12	12	9	6	9	8	2
APC MUTATED	4	10	8	8	5	7	7	2
APC WILD-TYPE	2	2	4	1	1	2	1	0

'APC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.498 (Fisher's exact test), Q value = 1

Table S3. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	13	11	15
APC MUTATED	25	11	9	10
APC WILD-TYPE	4	2	2	5

'APC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 1

Table S4. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	16	14	23
APC MUTATED	11	12	20
APC WILD-TYPE	5	2	3

'APC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S5. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	9	14	2	8
APC MUTATED	15	7	12	1	8
APC WILD-TYPE	5	2	2	1	0

'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.243 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	1	4	2	61
APC MUTATED	0	4	2	50
APC WILD-TYPE	1	0	0	11

'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S7. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_2	CLUS_3	CLUS_4
ALL	1	38	29
APC MUTATED	1	31	24
APC WILD-TYPE	0	7	5

'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_3	CLUS_4	CLUS_5
ALL	2	3	6	54
APC MUTATED	1	3	5	45
APC WILD-TYPE	1	0	1	9

'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.627 (Fisher's exact test), Q value = 1

Table S9. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	3	53
APC MUTATED	8	2	44
APC WILD-TYPE	1	1	9

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.014

Table S10. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	21	19
TP53 MUTATED	7	15	17
TP53 WILD-TYPE	17	6	2

Figure S1. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 1

Table S11. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	6	12	12	9	6	9	8	2
TP53 MUTATED	2	8	4	9	5	6	5	0
TP53 WILD-TYPE	4	4	8	0	1	3	3	2

Figure S2. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 1

Table S12. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	13	11	15
TP53 MUTATED	15	9	10	9
TP53 WILD-TYPE	14	4	1	6

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.161 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	16	14	23
TP53 MUTATED	10	12	13
TP53 WILD-TYPE	6	2	10

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.843 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	9	14	2	8
TP53 MUTATED	12	7	9	1	6
TP53 WILD-TYPE	8	2	5	1	2

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.488 (Fisher's exact test), Q value = 1

Table S15. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	1	4	2	61
TP53 MUTATED	0	2	1	40
TP53 WILD-TYPE	1	2	1	21

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.654 (Fisher's exact test), Q value = 1

Table S16. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_2	CLUS_3	CLUS_4
ALL	1	38	29
TP53 MUTATED	1	22	20
TP53 WILD-TYPE	0	16	9

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S17. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_3	CLUS_4	CLUS_5
ALL	2	3	6	54
TP53 MUTATED	1	2	4	34
TP53 WILD-TYPE	1	1	2	20

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 1

Table S18. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	3	53
TP53 MUTATED	8	1	32
TP53 WILD-TYPE	1	2	21

'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.248 (Fisher's exact test), Q value = 1

Table S19. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	21	19
KRAS MUTATED	16	11	8
KRAS WILD-TYPE	8	10	11

'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00762 (Fisher's exact test), Q value = 0.74

Table S20. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	6	12	12	9	6	9	8	2
KRAS MUTATED	3	9	9	3	3	6	0	2
KRAS WILD-TYPE	3	3	3	6	3	3	8	0

Figure S3. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00722 (Fisher's exact test), Q value = 0.71

Table S21. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	13	11	15
KRAS MUTATED	21	9	2	6
KRAS WILD-TYPE	8	4	9	9

Figure S4. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.831 (Fisher's exact test), Q value = 1

Table S22. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	16	14	23
KRAS MUTATED	7	8	12
KRAS WILD-TYPE	9	6	11

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.854 (Fisher's exact test), Q value = 1

Table S23. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	9	14	2	8
KRAS MUTATED	9	4	9	1	4
KRAS WILD-TYPE	11	5	5	1	4

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 1

Table S24. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	1	4	2	61
KRAS MUTATED	1	4	0	32
KRAS WILD-TYPE	0	0	2	29

Figure S5. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.013

Table S25. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_2	CLUS_3	CLUS_4
ALL	1	38	29
KRAS MUTATED	1	28	8
KRAS WILD-TYPE	0	10	21

Figure S6. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 1

Table S26. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_3	CLUS_4	CLUS_5
ALL	2	3	6	54
KRAS MUTATED	1	2	1	30
KRAS WILD-TYPE	1	1	5	24

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00615 (Fisher's exact test), Q value = 0.61

Table S27. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	3	53
KRAS MUTATED	1	3	30
KRAS WILD-TYPE	8	0	23

Figure S7. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

'SMAD4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.079 (Fisher's exact test), Q value = 1

Table S28. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	21	19
SMAD4 MUTATED	5	0	2
SMAD4 WILD-TYPE	19	21	17

'SMAD4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.779 (Fisher's exact test), Q value = 1

Table S29. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	6	12	12	9	6	9	8	2
SMAD4 MUTATED	0	3	2	1	0	1	0	0
SMAD4 WILD-TYPE	6	9	10	8	6	8	8	2

'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S30. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	13	11	15
SMAD4 MUTATED	4	1	1	2
SMAD4 WILD-TYPE	25	12	10	13

'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 1

Table S31. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	16	14	23
SMAD4 MUTATED	0	3	4
SMAD4 WILD-TYPE	16	11	19

'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0556 (Fisher's exact test), Q value = 1

Table S32. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	9	14	2	8
SMAD4 MUTATED	0	3	3	0	1
SMAD4 WILD-TYPE	20	6	11	2	7

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.188 (Fisher's exact test), Q value = 1

Table S33. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	1	4	2	61
SMAD4 MUTATED	1	0	0	7
SMAD4 WILD-TYPE	0	4	2	54

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.229 (Fisher's exact test), Q value = 1

Table S34. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_2	CLUS_3	CLUS_4
ALL	1	38	29
SMAD4 MUTATED	0	7	1
SMAD4 WILD-TYPE	1	31	28

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.309 (Fisher's exact test), Q value = 1

Table S35. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_3	CLUS_4	CLUS_5
ALL	2	3	6	54
SMAD4 MUTATED	1	0	0	7
SMAD4 WILD-TYPE	1	3	6	47

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.264 (Fisher's exact test), Q value = 1

Table S36. Gene #4: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	3	53
SMAD4 MUTATED	0	1	7
SMAD4 WILD-TYPE	9	2	46

'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 1

Table S37. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	21	19
FBXW7 MUTATED	2	5	1
FBXW7 WILD-TYPE	22	16	18

'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.41 (Fisher's exact test), Q value = 1

Table S38. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	6	12	12	9	6	9	8	2
FBXW7 MUTATED	0	3	1	1	0	3	0	0
FBXW7 WILD-TYPE	6	9	11	8	6	6	8	2

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.41 (Fisher's exact test), Q value = 1

Table S39. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	13	11	15
FBXW7 MUTATED	5	0	1	3
FBXW7 WILD-TYPE	24	13	10	12

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.69 (Fisher's exact test), Q value = 1

Table S40. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	16	14	23
FBXW7 MUTATED	3	2	2
FBXW7 WILD-TYPE	13	12	21

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.632 (Fisher's exact test), Q value = 1

Table S41. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	9	14	2	8
FBXW7 MUTATED	2	2	1	0	2
FBXW7 WILD-TYPE	18	7	13	2	6

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S42. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	1	4	2	61
FBXW7 MUTATED	0	0	0	9
FBXW7 WILD-TYPE	1	4	2	52

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.117 (Fisher's exact test), Q value = 1

Table S43. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_2	CLUS_3	CLUS_4
ALL	1	38	29
FBXW7 MUTATED	0	8	1
FBXW7 WILD-TYPE	1	30	28

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.804 (Fisher's exact test), Q value = 1

Table S44. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_3	CLUS_4	CLUS_5
ALL	2	3	6	54
FBXW7 MUTATED	0	0	0	9
FBXW7 WILD-TYPE	2	3	6	45

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.576 (Fisher's exact test), Q value = 1

Table S45. Gene #5: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	3	53
FBXW7 MUTATED	0	0	9
FBXW7 WILD-TYPE	9	3	44

'NRAS MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S46. Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	21	19
NRAS MUTATED	2	2	1
NRAS WILD-TYPE	22	19	18

'NRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.841 (Fisher's exact test), Q value = 1

Table S47. Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	6	12	12	9	6	9	8	2
NRAS MUTATED	1	2	1	1	0	0	0	0
NRAS WILD-TYPE	5	10	11	8	6	9	8	2

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.737 (Fisher's exact test), Q value = 1

Table S48. Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	13	11	15
NRAS MUTATED	3	1	1	0
NRAS WILD-TYPE	26	12	10	15

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S49. Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	1	4	2	61
NRAS MUTATED	0	0	0	5
NRAS WILD-TYPE	1	4	2	56

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S50. Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_2	CLUS_3	CLUS_4
ALL	1	38	29
NRAS MUTATED	0	3	2
NRAS WILD-TYPE	1	35	27

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0973 (Fisher's exact test), Q value = 1

Table S51. Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_3	CLUS_4	CLUS_5
ALL	2	3	6	54
NRAS MUTATED	1	0	1	3
NRAS WILD-TYPE	1	3	5	51

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S52. Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	3	53
NRAS MUTATED	0	0	5
NRAS WILD-TYPE	9	3	48

'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.364 (Fisher's exact test), Q value = 1

Table S53. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	21	19
ARID1A MUTATED	3	2	0
ARID1A WILD-TYPE	21	19	19

'ARID1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.392 (Fisher's exact test), Q value = 1

Table S54. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	6	12	12	9	6	9	8	2
ARID1A MUTATED	1	1	1	0	0	1	0	1
ARID1A WILD-TYPE	5	11	11	9	6	8	8	1

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.917 (Fisher's exact test), Q value = 1

Table S55. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	13	11	15
ARID1A MUTATED	3	1	0	1
ARID1A WILD-TYPE	26	12	11	14

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.173 (Fisher's exact test), Q value = 1

Table S56. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	16	14	23
ARID1A MUTATED	2	1	0
ARID1A WILD-TYPE	14	13	23

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.531 (Fisher's exact test), Q value = 1

Table S57. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	9	14	2	8
ARID1A MUTATED	2	0	0	0	1
ARID1A WILD-TYPE	18	9	14	2	7

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S58. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	1	4	2	61
ARID1A MUTATED	0	0	0	5
ARID1A WILD-TYPE	1	4	2	56

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S59. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_2	CLUS_3	CLUS_4
ALL	1	38	29
ARID1A MUTATED	0	3	2
ARID1A WILD-TYPE	1	35	27

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.314 (Fisher's exact test), Q value = 1

Table S60. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_3	CLUS_4	CLUS_5
ALL	2	3	6	54
ARID1A MUTATED	0	1	0	3
ARID1A WILD-TYPE	2	2	6	51

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S61. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	3	53
ARID1A MUTATED	0	1	3
ARID1A WILD-TYPE	9	2	50

'RBM10 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S62. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	21	19
RBM10 MUTATED	2	1	1
RBM10 WILD-TYPE	22	20	18

'RBM10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.788 (Fisher's exact test), Q value = 1

Table S63. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	6	12	12	9	6	9	8	2
RBM10 MUTATED	1	1	0	1	0	1	0	0
RBM10 WILD-TYPE	5	11	12	8	6	8	8	2

'RBM10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S64. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	13	11	15
RBM10 MUTATED	2	1	0	1
RBM10 WILD-TYPE	27	12	11	14

'RBM10 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S65. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	16	14	23
RBM10 MUTATED	1	1	1
RBM10 WILD-TYPE	15	13	22

'RBM10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.779 (Fisher's exact test), Q value = 1

Table S66. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	9	14	2	8
RBM10 MUTATED	1	0	1	0	1
RBM10 WILD-TYPE	19	9	13	2	7

'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 1

Table S67. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	1	4	2	61
RBM10 MUTATED	0	2	0	1
RBM10 WILD-TYPE	1	2	2	60

Figure S8. Get High-res Image Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0438 (Fisher's exact test), Q value = 1

Table S68. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_2	CLUS_3	CLUS_4
ALL	1	38	29
RBM10 MUTATED	1	1	1
RBM10 WILD-TYPE	0	37	28

Figure S9. Get High-res Image Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

'RBM10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.532 (Fisher's exact test), Q value = 1

Table S69. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_3	CLUS_4	CLUS_5
ALL	2	3	6	54
RBM10 MUTATED	0	0	1	3
RBM10 WILD-TYPE	2	3	5	51

'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.567 (Fisher's exact test), Q value = 1

Table S70. Gene #8: 'RBM10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	3	53
RBM10 MUTATED	1	0	3
RBM10 WILD-TYPE	8	3	50

'TCF7L2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.782 (Fisher's exact test), Q value = 1

Table S71. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	21	19
TCF7L2 MUTATED	2	2	3
TCF7L2 WILD-TYPE	22	19	16

'TCF7L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.208 (Fisher's exact test), Q value = 1

Table S72. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	6	12	12	9	6	9	8	2
TCF7L2 MUTATED	1	0	1	1	1	0	3	0
TCF7L2 WILD-TYPE	5	12	11	8	5	9	5	2

'TCF7L2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S73. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	13	11	15
TCF7L2 MUTATED	3	1	1	2
TCF7L2 WILD-TYPE	26	12	10	13

'TCF7L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.153 (Fisher's exact test), Q value = 1

Table S74. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	16	14	23
TCF7L2 MUTATED	2	2	0
TCF7L2 WILD-TYPE	14	12	23

'TCF7L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.292 (Fisher's exact test), Q value = 1

Table S75. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	9	14	2	8
TCF7L2 MUTATED	2	0	0	0	2
TCF7L2 WILD-TYPE	18	9	14	2	6

'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S76. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	1	4	2	61
TCF7L2 MUTATED	0	0	0	7
TCF7L2 WILD-TYPE	1	4	2	54

'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.305 (Fisher's exact test), Q value = 1

Table S77. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_2	CLUS_3	CLUS_4
ALL	1	38	29
TCF7L2 MUTATED	0	2	5
TCF7L2 WILD-TYPE	1	36	24

'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S78. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_3	CLUS_4	CLUS_5
ALL	2	3	6	54
TCF7L2 MUTATED	0	0	0	6
TCF7L2 WILD-TYPE	2	3	6	48

'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S79. Gene #9: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	3	53
TCF7L2 MUTATED	0	0	6
TCF7L2 WILD-TYPE	9	3	47

'ERBB2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S80. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	21	19
ERBB2 MUTATED	2	1	1
ERBB2 WILD-TYPE	22	20	18

'ERBB2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.875 (Fisher's exact test), Q value = 1

Table S81. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	6	12	12	9	6	9	8	2
ERBB2 MUTATED	0	1	2	1	0	0	0	0
ERBB2 WILD-TYPE	6	11	10	8	6	9	8	2

'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S82. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	13	11	15
ERBB2 MUTATED	2	1	0	1
ERBB2 WILD-TYPE	27	12	11	14

'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.673 (Fisher's exact test), Q value = 1

Table S83. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	16	14	23
ERBB2 MUTATED	1	2	1
ERBB2 WILD-TYPE	15	12	22

'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S84. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	9	14	2	8
ERBB2 MUTATED	1	0	1	0	2
ERBB2 WILD-TYPE	19	9	13	2	6

'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 1

Table S85. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	1	4	2	61
ERBB2 MUTATED	0	2	0	2
ERBB2 WILD-TYPE	1	2	2	59

Figure S10. Get High-res Image Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0331 (Fisher's exact test), Q value = 1

Table S86. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_2	CLUS_3	CLUS_4
ALL	1	38	29
ERBB2 MUTATED	1	1	2
ERBB2 WILD-TYPE	0	37	27

Figure S11. Get High-res Image Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S87. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_3	CLUS_4	CLUS_5
ALL	2	3	6	54
ERBB2 MUTATED	0	0	0	3
ERBB2 WILD-TYPE	2	3	6	51

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S88. Gene #10: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	3	53
ERBB2 MUTATED	0	0	3
ERBB2 WILD-TYPE	9	3	50

'KIAA1804 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.51 (Fisher's exact test), Q value = 1

Table S89. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	21	19
KIAA1804 MUTATED	3	4	1
KIAA1804 WILD-TYPE	21	17	18

'KIAA1804 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.835 (Fisher's exact test), Q value = 1

Table S90. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	6	12	12	9	6	9	8	2
KIAA1804 MUTATED	0	1	3	1	0	2	1	0
KIAA1804 WILD-TYPE	6	11	9	8	6	7	7	2

'KIAA1804 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 1

Table S91. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	13	11	15
KIAA1804 MUTATED	8	0	0	1
KIAA1804 WILD-TYPE	21	13	11	14

Figure S12. Get High-res Image Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KIAA1804 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S92. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	16	14	23
KIAA1804 MUTATED	2	2	4
KIAA1804 WILD-TYPE	14	12	19

'KIAA1804 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.596 (Fisher's exact test), Q value = 1

Table S93. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	9	14	2	8
KIAA1804 MUTATED	3	0	3	0	2
KIAA1804 WILD-TYPE	17	9	11	2	6

'KIAA1804 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S94. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	1	4	2	61
KIAA1804 MUTATED	0	0	0	9
KIAA1804 WILD-TYPE	1	4	2	52

'KIAA1804 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.761 (Fisher's exact test), Q value = 1

Table S95. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_2	CLUS_3	CLUS_4
ALL	1	38	29
KIAA1804 MUTATED	0	6	3
KIAA1804 WILD-TYPE	1	32	26

'KIAA1804 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.806 (Fisher's exact test), Q value = 1

Table S96. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_3	CLUS_4	CLUS_5
ALL	2	3	6	54
KIAA1804 MUTATED	0	0	0	9
KIAA1804 WILD-TYPE	2	3	6	45

'KIAA1804 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.576 (Fisher's exact test), Q value = 1

Table S97. Gene #11: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	3	53
KIAA1804 MUTATED	0	0	9
KIAA1804 WILD-TYPE	9	3	44

'CCDC88C MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S98. Gene #12: 'CCDC88C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	1	4	2	61
CCDC88C MUTATED	0	0	0	3
CCDC88C WILD-TYPE	1	4	2	58

'CCDC88C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.596 (Fisher's exact test), Q value = 1

Table S99. Gene #12: 'CCDC88C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_2	CLUS_3	CLUS_4
ALL	1	38	29
CCDC88C MUTATED	0	1	2
CCDC88C WILD-TYPE	1	37	27

'CCDC88C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.432 (Fisher's exact test), Q value = 1

Table S100. Gene #12: 'CCDC88C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_3	CLUS_4	CLUS_5
ALL	2	3	6	54
CCDC88C MUTATED	0	0	1	2
CCDC88C WILD-TYPE	2	3	5	52

'CCDC88C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S101. Gene #12: 'CCDC88C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	3	53
CCDC88C MUTATED	1	0	2
CCDC88C WILD-TYPE	8	3	51

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = READ-TP.transferedmergedcluster.txt
Number of patients = 69
Number of significantly mutated genes = 12
Number of Molecular subtypes = 9
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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