Correlation between gene mutation status and molecular subtypes

Head and Neck Squamous Cell Carcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_23

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 (2013): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1CJ8BHW

Overview

Introduction

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

Summary

Testing the association between mutation status of 45 genes and 10 molecular subtypes across 306 patients, 19 significant findings detected with P value < 0.05 and Q value < 0.25.

NSD1 mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
HRAS mutation correlated to 'CN_CNMF'.
TP53 mutation correlated to 'CN_CNMF'.
NOTCH1 mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
CASP8 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
EPHA2 mutation correlated to 'MIRSEQ_MATURE_CNMF'.
CSMD3 mutation correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 45 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, 19 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	Chi-square 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
CASP8	27 (9%)	279	1.62e-05 (0.00695)	0.000335 (0.142)	0.699 (1.00)	0.739 (1.00)	3e-07 (0.000131)	5.28e-07 (0.00023)	0.377 (1.00)	0.564 (1.00)	0.000302 (0.128)	0.0244 (1.00)
NOTCH1	57 (19%)	249	0.88 (1.00)	0.000562 (0.236)	0.0187 (1.00)	0.279 (1.00)	0.000428 (0.181)	2.54e-06 (0.0011)	0.000112 (0.0481)	0.292 (1.00)	0.000786 (0.329)	0.0017 (0.703)
CSMD3	70 (23%)	236	0.0549 (1.00)	0.00234 (0.965)	0.00973 (1.00)	0.463 (1.00)	1.35e-05 (0.00583)	6.66e-07 (0.00029)	0.000542 (0.228)	0.00103 (0.429)	0.000137 (0.0586)	0.00299 (1.00)
NSD1	33 (11%)	273	0.302 (1.00)	1.27e-05 (0.0055)	0.244 (1.00)	0.73 (1.00)	0.000411 (0.174)	6.41e-06 (0.00277)	0.00974 (1.00)	0.0355 (1.00)	0.0297 (1.00)	0.0072 (1.00)
HRAS	10 (3%)	296	8.17e-05 (0.0351)	0.0261 (1.00)	0.168 (1.00)	0.599 (1.00)	0.00339 (1.00)	0.0011 (0.457)	0.0991 (1.00)	0.188 (1.00)	0.0484 (1.00)	0.21 (1.00)
TP53	214 (70%)	92	1.7e-12 (7.44e-10)	0.00948 (1.00)	0.11 (1.00)	0.776 (1.00)	0.0113 (1.00)	0.00143 (0.592)	0.0611 (1.00)	0.0008 (0.334)	0.0417 (1.00)	0.00811 (1.00)
EPHA2	14 (5%)	292	0.111 (1.00)	0.00794 (1.00)	0.811 (1.00)	0.906 (1.00)	0.499 (1.00)	0.57 (1.00)	0.775 (1.00)	0.184 (1.00)	0.000357 (0.151)	0.0592 (1.00)
PIK3CA	64 (21%)	242	0.0654 (1.00)	0.0334 (1.00)	0.0948 (1.00)	0.928 (1.00)	0.119 (1.00)	0.398 (1.00)	0.038 (1.00)	0.0446 (1.00)	0.0942 (1.00)	0.304 (1.00)
CDKN2A	65 (21%)	241	0.022 (1.00)	0.494 (1.00)	0.0349 (1.00)	0.583 (1.00)	0.201 (1.00)	0.206 (1.00)	0.418 (1.00)	0.113 (1.00)	0.191 (1.00)	0.15 (1.00)
NFE2L2	17 (6%)	289	0.807 (1.00)	0.267 (1.00)	0.125 (1.00)	0.765 (1.00)	1 (1.00)	0.464 (1.00)	0.248 (1.00)	0.0736 (1.00)	0.357 (1.00)	0.471 (1.00)
FAT1	72 (24%)	234	0.24 (1.00)	0.621 (1.00)	0.794 (1.00)	0.487 (1.00)	0.152 (1.00)	0.288 (1.00)	0.885 (1.00)	0.317 (1.00)	0.162 (1.00)	0.151 (1.00)
JUB	18 (6%)	288	0.201 (1.00)	0.181 (1.00)	0.0646 (1.00)	0.0816 (1.00)	0.305 (1.00)	0.221 (1.00)	0.328 (1.00)	1 (1.00)	0.0121 (1.00)	0.706 (1.00)
MLL2	56 (18%)	250	0.0727 (1.00)	0.00657 (1.00)	0.687 (1.00)	0.521 (1.00)	0.0532 (1.00)	0.00795 (1.00)	0.0529 (1.00)	0.0102 (1.00)	0.225 (1.00)	0.0303 (1.00)
FBXW7	15 (5%)	291	0.76 (1.00)	0.851 (1.00)	0.092 (1.00)	0.303 (1.00)	0.881 (1.00)	0.636 (1.00)	0.945 (1.00)	0.854 (1.00)	0.872 (1.00)	0.804 (1.00)
ZNF750	13 (4%)	293	0.396 (1.00)	0.00628 (1.00)	0.946 (1.00)	0.353 (1.00)	0.119 (1.00)	0.128 (1.00)	0.632 (1.00)	1 (1.00)	0.29 (1.00)	0.692 (1.00)
FLG	48 (16%)	258	0.733 (1.00)	0.0404 (1.00)	0.532 (1.00)	0.575 (1.00)	0.139 (1.00)	0.223 (1.00)	0.0631 (1.00)	0.163 (1.00)	0.0672 (1.00)	0.275 (1.00)
B2M	7 (2%)	299	0.241 (1.00)	0.225 (1.00)			0.515 (1.00)	0.517 (1.00)	0.141 (1.00)	0.756 (1.00)	0.157 (1.00)	0.499 (1.00)
IL32	4 (1%)	302	0.0451 (1.00)	0.129 (1.00)			0.561 (1.00)	1 (1.00)	0.561 (1.00)	0.669 (1.00)	0.828 (1.00)	1 (1.00)
EP300	25 (8%)	281	0.0376 (1.00)	0.728 (1.00)	0.769 (1.00)	0.264 (1.00)	0.00955 (1.00)	0.00467 (1.00)	0.352 (1.00)	0.335 (1.00)	0.232 (1.00)	0.026 (1.00)
RHOA	4 (1%)	302	0.724 (1.00)	0.177 (1.00)	0.379 (1.00)	0.444 (1.00)	0.245 (1.00)	0.141 (1.00)	0.246 (1.00)	0.231 (1.00)	0.139 (1.00)	0.361 (1.00)
HLA-A	9 (3%)	297	0.916 (1.00)	0.711 (1.00)	1 (1.00)	1 (1.00)	0.072 (1.00)	0.0311 (1.00)	0.634 (1.00)	0.588 (1.00)	0.175 (1.00)	0.337 (1.00)
CTCF	11 (4%)	295	0.248 (1.00)	0.122 (1.00)	0.393 (1.00)	0.541 (1.00)	0.636 (1.00)	0.632 (1.00)	0.861 (1.00)	0.81 (1.00)	0.66 (1.00)	0.722 (1.00)
RB1	10 (3%)	296	0.0297 (1.00)	0.00888 (1.00)	0.282 (1.00)	0.129 (1.00)	0.00607 (1.00)	0.00838 (1.00)	0.0561 (1.00)	1 (1.00)	0.263 (1.00)	0.0707 (1.00)
TGFBR2	10 (3%)	296	0.0814 (1.00)	0.483 (1.00)	0.469 (1.00)	1 (1.00)	0.313 (1.00)	0.785 (1.00)	0.919 (1.00)	1 (1.00)	0.159 (1.00)	0.46 (1.00)
NECAB1	6 (2%)	300	0.0438 (1.00)	1 (1.00)	0.856 (1.00)	0.672 (1.00)	0.114 (1.00)	0.0622 (1.00)	0.773 (1.00)	0.49 (1.00)	0.769 (1.00)	0.45 (1.00)
KRTAP1-5	3 (1%)	303	0.927 (1.00)	1 (1.00)			0.78 (1.00)	0.63 (1.00)	0.0245 (1.00)	1 (1.00)	0.37 (1.00)	0.794 (1.00)
MAPK1	4 (1%)	302	0.808 (1.00)	0.698 (1.00)	0.569 (1.00)	1 (1.00)	0.691 (1.00)	0.686 (1.00)	0.69 (1.00)	0.669 (1.00)	0.685 (1.00)	0.713 (1.00)
PLSCR1	5 (2%)	301	0.329 (1.00)	0.291 (1.00)	1 (1.00)	1 (1.00)	0.524 (1.00)	0.526 (1.00)	0.157 (1.00)	0.442 (1.00)	0.739 (1.00)	0.761 (1.00)
CNPY3	3 (1%)	303	0.443 (1.00)	0.66 (1.00)			0.5 (1.00)	0.499 (1.00)	0.501 (1.00)	0.59 (1.00)	0.498 (1.00)	0.794 (1.00)
EPB41L3	16 (5%)	290	0.815 (1.00)	0.308 (1.00)	0.253 (1.00)	0.0152 (1.00)	0.0509 (1.00)	0.0132 (1.00)	0.154 (1.00)	0.202 (1.00)	0.161 (1.00)	0.185 (1.00)
RAC1	9 (3%)	297	0.302 (1.00)	1 (1.00)	1 (1.00)	0.519 (1.00)	0.195 (1.00)	0.192 (1.00)	0.218 (1.00)	0.321 (1.00)	0.496 (1.00)	0.332 (1.00)
CUL3	10 (3%)	296	0.82 (1.00)	0.336 (1.00)	0.737 (1.00)	0.636 (1.00)	0.403 (1.00)	0.852 (1.00)	0.79 (1.00)	0.359 (1.00)	0.904 (1.00)	0.567 (1.00)
TRPV4	7 (2%)	299	0.302 (1.00)	0.412 (1.00)	0.796 (1.00)	0.27 (1.00)	0.571 (1.00)	0.0634 (1.00)	0.569 (1.00)	0.371 (1.00)	0.714 (1.00)	0.332 (1.00)
PRB2	10 (3%)	296	0.499 (1.00)	0.0801 (1.00)	0.888 (1.00)	1 (1.00)	0.669 (1.00)	0.231 (1.00)	0.667 (1.00)	0.15 (1.00)	0.235 (1.00)	0.164 (1.00)
PRB1	7 (2%)	299	0.568 (1.00)	0.639 (1.00)	0.757 (1.00)	0.672 (1.00)	0.89 (1.00)	0.639 (1.00)	0.106 (1.00)	1 (1.00)	0.157 (1.00)	0.797 (1.00)
WHSC1	10 (3%)	296	0.0792 (1.00)	0.112 (1.00)	0.284 (1.00)	0.622 (1.00)	0.855 (1.00)	0.852 (1.00)	0.174 (1.00)	1 (1.00)	0.0832 (1.00)	0.93 (1.00)
STEAP4	10 (3%)	296	0.292 (1.00)	0.0801 (1.00)	0.175 (1.00)	0.656 (1.00)	0.0813 (1.00)	0.0997 (1.00)	0.0817 (1.00)	1 (1.00)	0.109 (1.00)	0.137 (1.00)
HIST1H1B	7 (2%)	299	0.0466 (1.00)	0.152 (1.00)	0.705 (1.00)	0.822 (1.00)	0.802 (1.00)	0.717 (1.00)	0.569 (1.00)	0.108 (1.00)	0.89 (1.00)	0.131 (1.00)
KCNA3	8 (3%)	298	0.855 (1.00)	0.105 (1.00)	0.802 (1.00)	0.0518 (1.00)	0.606 (1.00)	0.491 (1.00)	0.907 (1.00)	0.306 (1.00)	0.582 (1.00)	0.503 (1.00)
EPDR1	6 (2%)	300	0.45 (1.00)	1 (1.00)	0.561 (1.00)	0.779 (1.00)	0.327 (1.00)	0.675 (1.00)	0.88 (1.00)	1 (1.00)	1 (1.00)	0.705 (1.00)
SLC26A7	8 (3%)	298	0.646 (1.00)	0.606 (1.00)	0.569 (1.00)	0.209 (1.00)	0.2 (1.00)	0.311 (1.00)	0.907 (1.00)	0.764 (1.00)	1 (1.00)	0.828 (1.00)
OR8D4	6 (2%)	300	0.927 (1.00)	0.618 (1.00)	0.894 (1.00)	0.438 (1.00)	0.387 (1.00)	1 (1.00)	0.387 (1.00)	0.72 (1.00)	0.328 (1.00)	0.264 (1.00)
POU4F2	7 (2%)	299	0.671 (1.00)	0.802 (1.00)	0.428 (1.00)	0.404 (1.00)	0.571 (1.00)	0.563 (1.00)	0.344 (1.00)	0.756 (1.00)	0.304 (1.00)	0.332 (1.00)
FCRL4	13 (4%)	293	0.677 (1.00)	0.406 (1.00)	0.788 (1.00)	1 (1.00)	0.405 (1.00)	0.106 (1.00)	0.377 (1.00)	0.833 (1.00)	0.43 (1.00)	0.572 (1.00)
TXK	3 (1%)	303	0.417 (1.00)	0.547 (1.00)			0.78 (1.00)	0.782 (1.00)	0.114 (1.00)	1 (1.00)

'NSD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.0055

Table S1. Gene #1: 'NSD1 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	104	102
NSD1 MUTATED	22	9	2
NSD1 WILD-TYPE	78	95	100

Figure S1. Get High-res Image Gene #1: 'NSD1 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'NSD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000411 (Fisher's exact test), Q value = 0.17

Table S2. Gene #1: 'NSD1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	93	89
NSD1 MUTATED	23	3	7
NSD1 WILD-TYPE	94	90	82

Figure S2. Get High-res Image Gene #1: 'NSD1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'NSD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.41e-06 (Fisher's exact test), Q value = 0.0028

Table S3. Gene #1: 'NSD1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	84	118
NSD1 MUTATED	3	4	26
NSD1 WILD-TYPE	94	80	92

Figure S3. Get High-res Image Gene #1: 'NSD1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 8.17e-05 (Chi-square test), Q value = 0.035

Table S4. Gene #4: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	70	47	63	26	58	17	6	15
HRAS MUTATED	0	0	9	0	1	0	0	0
HRAS WILD-TYPE	70	47	54	26	57	17	6	15

Figure S4. Get High-res Image Gene #4: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.7e-12 (Chi-square test), Q value = 7.4e-10

Table S5. Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	70	47	63	26	58	17	6	15
TP53 MUTATED	59	36	20	14	47	16	6	14
TP53 WILD-TYPE	11	11	43	12	11	1	0	1

Figure S5. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000562 (Fisher's exact test), Q value = 0.24

Table S6. Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	104	102
NOTCH1 MUTATED	18	9	30
NOTCH1 WILD-TYPE	82	95	72

Figure S6. Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000428 (Fisher's exact test), Q value = 0.18

Table S7. Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	93	89
NOTCH1 MUTATED	10	22	25
NOTCH1 WILD-TYPE	107	71	64

Figure S7. Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.54e-06 (Fisher's exact test), Q value = 0.0011

Table S8. Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	84	118
NOTCH1 MUTATED	20	29	8
NOTCH1 WILD-TYPE	77	55	110

Figure S8. Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000112 (Fisher's exact test), Q value = 0.048

Table S9. Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	119	96
NOTCH1 MUTATED	26	9	21
NOTCH1 WILD-TYPE	63	110	75

Figure S9. Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.62e-05 (Chi-square test), Q value = 0.0069

Table S10. Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	70	47	63	26	58	17	6	15
CASP8 MUTATED	1	0	16	3	4	1	1	0
CASP8 WILD-TYPE	69	47	47	23	54	16	5	15

Figure S10. Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000335 (Fisher's exact test), Q value = 0.14

Table S11. Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	104	102
CASP8 MUTATED	11	1	15
CASP8 WILD-TYPE	89	103	87

Figure S11. Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3e-07 (Fisher's exact test), Q value = 0.00013

Table S12. Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	93	89
CASP8 MUTATED	1	5	19
CASP8 WILD-TYPE	116	88	70

Figure S12. Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.28e-07 (Fisher's exact test), Q value = 0.00023

Table S13. Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	84	118
CASP8 MUTATED	6	18	1
CASP8 WILD-TYPE	91	66	117

Figure S13. Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000302 (Fisher's exact test), Q value = 0.13

Table S14. Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	106	88
CASP8 MUTATED	14	2	8
CASP8 WILD-TYPE	60	104	80

Figure S14. Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000357 (Fisher's exact test), Q value = 0.15

Table S15. Gene #13: 'EPHA2 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	106	88
EPHA2 MUTATED	8	0	2
EPHA2 WILD-TYPE	66	106	86

Figure S15. Get High-res Image Gene #13: 'EPHA2 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

'CSMD3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.35e-05 (Fisher's exact test), Q value = 0.0058

Table S16. Gene #24: 'CSMD3 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	93	89
CSMD3 MUTATED	43	9	18
CSMD3 WILD-TYPE	74	84	71

Figure S16. Get High-res Image Gene #24: 'CSMD3 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'CSMD3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.66e-07 (Fisher's exact test), Q value = 0.00029

Table S17. Gene #24: 'CSMD3 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	84	118
CSMD3 MUTATED	9	15	46
CSMD3 WILD-TYPE	88	69	72

Figure S17. Get High-res Image Gene #24: 'CSMD3 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'CSMD3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000542 (Fisher's exact test), Q value = 0.23

Table S18. Gene #24: 'CSMD3 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	119	96
CSMD3 MUTATED	22	38	10
CSMD3 WILD-TYPE	67	81	86

Figure S18. Get High-res Image Gene #24: 'CSMD3 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'CSMD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000137 (Fisher's exact test), Q value = 0.059

Table S19. Gene #24: 'CSMD3 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	106	88
CSMD3 MUTATED	16	34	7
CSMD3 WILD-TYPE	58	72	81

Figure S19. Get High-res Image Gene #24: 'CSMD3 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

Methods & Data

Input

Mutation data file = HNSC-TP.mutsig.cluster.txt
Molecular subtypes file = HNSC-TP.transferedmergedcluster.txt
Number of patients = 306
Number of significantly mutated genes = 45
Number of Molecular subtypes = 10
Exclude genes that fewer than K tumors have mutations, K = 3

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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References

[1] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[2] 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)

[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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