Correlation between gene mutation status and molecular subtypes

Colon Adenocarcinoma (Primary solid tumor)

22 February 2013 | analyses__2013_02_22

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/C1R78CCT

Overview

Introduction

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

Summary

Testing the association between mutation status of 120 genes and 9 molecular subtypes across 155 patients, 19 significant findings detected with P value < 0.05 and Q value < 0.25.

BRAF mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
KRAS mutation correlated to 'MRNA_CHIERARCHICAL' and 'MRNASEQ_CNMF'.
TP53 mutation correlated to 'CN_CNMF'.
FAT4 mutation correlated to 'CN_CNMF'.
OR6N1 mutation correlated to 'MRNA_CNMF'.
FLG mutation correlated to 'MRNA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
OR51V1 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.
DNAH5 mutation correlated to 'MRNA_CNMF'.
CASP8 mutation correlated to 'MRNA_CHIERARCHICAL' and 'MRNASEQ_CHIERARCHICAL'.
ZC3H13 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.
TMEM132D mutation correlated to 'MRNA_CNMF'.
SYNE1 mutation correlated to 'MRNA_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 120 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, 19 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
BRAF	20 (13%)	135	7.27e-06 (0.00728)	5.29e-07 (0.00053)	8.5e-05 (0.0846)	0.608 (1.00)	0.438 (1.00)	7.22e-08 (7.25e-05)	1.15e-07 (0.000116)	0.145 (1.00)	1 (1.00)
KRAS	58 (37%)	97	0.0147 (1.00)	0.000215 (0.212)	0.15 (1.00)	0.521 (1.00)	0.298 (1.00)	9.44e-08 (9.48e-05)	0.765 (1.00)	1 (1.00)	0.613 (1.00)
FLG	26 (17%)	129	0.000162 (0.16)	0.00765 (1.00)	0.00027 (0.267)	0.0685 (1.00)	0.653 (1.00)	0.000746 (0.728)	9.69e-05 (0.0963)	1 (1.00)	0.61 (1.00)
CASP8	10 (6%)	145	0.000601 (0.587)	4e-05 (0.0399)	0.00174 (1.00)	0.34 (1.00)	1 (1.00)	0.000598 (0.585)	5.75e-05 (0.0573)	1 (1.00)	0.255 (1.00)
TP53	75 (48%)	80	0.00691 (1.00)	0.00861 (1.00)	1.08e-09 (1.09e-06)	0.249 (1.00)	0.894 (1.00)	0.00325 (1.00)	0.0669 (1.00)	0.366 (1.00)	0.807 (1.00)
FAT4	29 (19%)	126	0.0063 (1.00)	0.0115 (1.00)	0.000172 (0.171)	0.178 (1.00)	0.748 (1.00)	0.0487 (1.00)	0.00492 (1.00)	0.241 (1.00)	0.0218 (1.00)
OR6N1	8 (5%)	147	0.000126 (0.125)	0.0404 (1.00)	0.00971 (1.00)			0.0184 (1.00)	0.00873 (1.00)	0.226 (1.00)	1 (1.00)
OR51V1	9 (6%)	146	0.00559 (1.00)	0.0173 (1.00)	0.00436 (1.00)	0.272 (1.00)	1 (1.00)	0.00736 (1.00)	0.000158 (0.156)	1 (1.00)	0.283 (1.00)
DNAH5	28 (18%)	127	8.23e-06 (0.00823)	0.00232 (1.00)	0.0134 (1.00)	0.159 (1.00)	0.518 (1.00)	0.00104 (1.00)	0.00176 (1.00)	0.585 (1.00)	0.642 (1.00)
ZC3H13	17 (11%)	138	0.00312 (1.00)	0.000953 (0.926)	0.00682 (1.00)	0.371 (1.00)	0.353 (1.00)	0.0745 (1.00)	1.8e-05 (0.018)	1 (1.00)	0.41 (1.00)
TMEM132D	15 (10%)	140	4.92e-05 (0.049)	0.000829 (0.807)	0.0272 (1.00)	0.371 (1.00)	1 (1.00)	0.0175 (1.00)	0.0306 (1.00)	1 (1.00)	1 (1.00)
SYNE1	37 (24%)	118	0.000178 (0.176)	0.000788 (0.768)	0.000289 (0.284)	0.418 (1.00)	0.744 (1.00)	0.00318 (1.00)	0.00136 (1.00)	1 (1.00)	0.181 (1.00)
APC	103 (66%)	52	0.0865 (1.00)	0.0683 (1.00)	0.101 (1.00)	0.167 (1.00)	0.598 (1.00)	0.0715 (1.00)	0.528 (1.00)	1 (1.00)	1 (1.00)
FBXW7	29 (19%)	126	0.201 (1.00)	0.208 (1.00)	0.000825 (0.803)	0.0226 (1.00)	0.024 (1.00)	0.00764 (1.00)	0.0261 (1.00)	0.583 (1.00)	0.657 (1.00)
NRAS	15 (10%)	140	0.124 (1.00)	0.42 (1.00)	0.531 (1.00)	0.368 (1.00)	0.438 (1.00)	0.395 (1.00)	0.528 (1.00)	1 (1.00)	1 (1.00)
PIK3CA	26 (17%)	129	0.303 (1.00)	0.655 (1.00)	0.0178 (1.00)	0.00804 (1.00)	0.0841 (1.00)	0.00435 (1.00)	0.532 (1.00)	1 (1.00)	0.592 (1.00)
SMAD4	18 (12%)	137	0.206 (1.00)	0.0104 (1.00)	0.01 (1.00)	0.539 (1.00)	0.125 (1.00)	0.0254 (1.00)	0.421 (1.00)	1 (1.00)	1 (1.00)
FAM123B	19 (12%)	136	0.116 (1.00)	0.0364 (1.00)	0.019 (1.00)	0.313 (1.00)	0.519 (1.00)	0.0296 (1.00)	0.0507 (1.00)	0.498 (1.00)	0.498 (1.00)
TTN	69 (45%)	86	0.00416 (1.00)	0.0142 (1.00)	0.0011 (1.00)	0.163 (1.00)	0.964 (1.00)	0.14 (1.00)	0.000308 (0.303)	0.655 (1.00)	0.793 (1.00)
WBSCR17	17 (11%)	138	0.509 (1.00)	0.568 (1.00)	0.388 (1.00)	0.19 (1.00)	0.321 (1.00)	0.704 (1.00)	0.276 (1.00)	0.109 (1.00)	0.109 (1.00)
ACVR1B	13 (8%)	142	0.269 (1.00)	0.507 (1.00)	0.00744 (1.00)	0.166 (1.00)	0.0496 (1.00)	0.115 (1.00)	0.00942 (1.00)	1 (1.00)	0.386 (1.00)
TNFRSF10C	6 (4%)	149	0.425 (1.00)	0.556 (1.00)	0.0811 (1.00)	0.663 (1.00)	0.162 (1.00)	0.783 (1.00)	0.656 (1.00)	1 (1.00)	1 (1.00)
SMAD2	10 (6%)	145	0.107 (1.00)	0.00374 (1.00)	0.0333 (1.00)	1 (1.00)	0.565 (1.00)	0.0413 (1.00)	0.0404 (1.00)	0.283 (1.00)	1 (1.00)
MAP2K4	9 (6%)	146	0.485 (1.00)	0.279 (1.00)	0.0512 (1.00)	0.405 (1.00)	0.757 (1.00)	0.0611 (1.00)	0.344 (1.00)	1 (1.00)	0.255 (1.00)
PCBP1	4 (3%)	151	0.381 (1.00)	0.574 (1.00)	0.486 (1.00)			0.183 (1.00)	0.753 (1.00)	1 (1.00)	1 (1.00)
LRP1B	30 (19%)	125	0.00356 (1.00)	0.00187 (1.00)	0.00112 (1.00)	0.608 (1.00)	0.867 (1.00)	0.000547 (0.536)	0.00359 (1.00)	1 (1.00)	0.00789 (1.00)
NRXN1	17 (11%)	138	0.334 (1.00)	0.458 (1.00)	0.0134 (1.00)	1 (1.00)	1 (1.00)	0.0898 (1.00)	0.109 (1.00)	1 (1.00)	0.455 (1.00)
GRIA1	14 (9%)	141	0.146 (1.00)	0.231 (1.00)	0.329 (1.00)			0.0738 (1.00)	0.0829 (1.00)	1 (1.00)	0.000411 (0.404)
SDK1	25 (16%)	130	0.0044 (1.00)	0.0014 (1.00)	0.31 (1.00)	1 (1.00)	0.908 (1.00)	0.0133 (1.00)	0.0271 (1.00)	1 (1.00)	0.575 (1.00)
SOX9	9 (6%)	146	0.263 (1.00)	0.18 (1.00)	0.585 (1.00)	0.697 (1.00)	1 (1.00)	0.445 (1.00)	0.257 (1.00)	1 (1.00)	1 (1.00)
DMD	27 (17%)	128	0.0146 (1.00)	0.0119 (1.00)	0.00855 (1.00)	0.474 (1.00)	0.174 (1.00)	0.0381 (1.00)	0.0188 (1.00)	1 (1.00)	0.0998 (1.00)
CNTN6	15 (10%)	140	0.133 (1.00)	0.235 (1.00)	0.329 (1.00)	0.34 (1.00)	0.674 (1.00)	0.812 (1.00)	0.121 (1.00)	1 (1.00)	0.361 (1.00)
GABRA5	8 (5%)	147	0.662 (1.00)	0.897 (1.00)	1 (1.00)			0.699 (1.00)	0.432 (1.00)	0.197 (1.00)	0.197 (1.00)
OR2M4	8 (5%)	147	0.00615 (1.00)	0.435 (1.00)	0.0771 (1.00)	0.34 (1.00)	0.674 (1.00)	0.0713 (1.00)	0.173 (1.00)	1 (1.00)	0.255 (1.00)
PCDH9	16 (10%)	139	0.462 (1.00)	0.799 (1.00)	0.354 (1.00)	0.238 (1.00)	0.757 (1.00)	0.174 (1.00)	0.845 (1.00)	1 (1.00)	0.41 (1.00)
TXNDC3	10 (6%)	145	0.1 (1.00)	0.298 (1.00)	0.0548 (1.00)	0.457 (1.00)	0.05 (1.00)	0.165 (1.00)	0.182 (1.00)	1 (1.00)	0.283 (1.00)
MGC26647	7 (5%)	148	0.273 (1.00)	0.947 (1.00)	0.887 (1.00)	0.395 (1.00)	0.674 (1.00)	0.521 (1.00)	0.486 (1.00)	1 (1.00)	0.166 (1.00)
FAM22F	8 (5%)	147	1 (1.00)	0.147 (1.00)	0.906 (1.00)	0.869 (1.00)	0.757 (1.00)	0.534 (1.00)	0.535 (1.00)	1 (1.00)	1 (1.00)
ACVR2A	8 (5%)	147	0.0213 (1.00)	0.46 (1.00)	0.098 (1.00)	0.148 (1.00)	0.246 (1.00)	0.202 (1.00)	0.0903 (1.00)	1 (1.00)	0.255 (1.00)
TCF7L2	11 (7%)	144	0.485 (1.00)	0.557 (1.00)	0.0875 (1.00)	0.604 (1.00)	1 (1.00)	0.198 (1.00)	0.389 (1.00)	1 (1.00)	0.283 (1.00)
AFF2	15 (10%)	140	0.0106 (1.00)	0.121 (1.00)	0.648 (1.00)	0.304 (1.00)	0.127 (1.00)	0.0341 (1.00)	0.909 (1.00)	0.41 (1.00)	0.41 (1.00)
CNBD1	6 (4%)	149	0.495 (1.00)	0.556 (1.00)	0.312 (1.00)			0.0897 (1.00)	0.258 (1.00)	1 (1.00)	0.197 (1.00)
OTOL1	7 (5%)	148	0.381 (1.00)	1 (1.00)	1 (1.00)			0.707 (1.00)	1 (1.00)	1 (1.00)	0.226 (1.00)
KCNA4	10 (6%)	145	0.0943 (1.00)	0.16 (1.00)	0.123 (1.00)	0.0501 (1.00)	0.179 (1.00)	0.256 (1.00)	0.00431 (1.00)	1 (1.00)	1 (1.00)
ISL1	8 (5%)	147	0.102 (1.00)	0.471 (1.00)	0.756 (1.00)	1 (1.00)	1 (1.00)	0.477 (1.00)	0.14 (1.00)	1 (1.00)	0.255 (1.00)
MGC42105	10 (6%)	145	0.00614 (1.00)	0.177 (1.00)	0.162 (1.00)	0.146 (1.00)	0.0748 (1.00)	0.122 (1.00)	0.182 (1.00)	1 (1.00)	1 (1.00)
ACOT4	3 (2%)	152	0.674 (1.00)	0.094 (1.00)	0.736 (1.00)			1 (1.00)	0.665 (1.00)	1 (1.00)	1 (1.00)
CDH11	13 (8%)	142	0.105 (1.00)	0.349 (1.00)	0.258 (1.00)	1 (1.00)	1 (1.00)	0.374 (1.00)	0.249 (1.00)	0.336 (1.00)	1 (1.00)
ATM	21 (14%)	134	0.148 (1.00)	0.351 (1.00)	0.00208 (1.00)	0.237 (1.00)	1 (1.00)	0.241 (1.00)	0.0513 (1.00)	1 (1.00)	0.0702 (1.00)
TPTE	11 (7%)	144	0.104 (1.00)	0.159 (1.00)	0.129 (1.00)	0.78 (1.00)	1 (1.00)	0.00614 (1.00)	0.121 (1.00)	1 (1.00)	0.31 (1.00)
BTNL8	3 (2%)	152	0.341 (1.00)	0.094 (1.00)	0.317 (1.00)	0.148 (1.00)	1 (1.00)	0.483 (1.00)	0.665 (1.00)	1 (1.00)	1 (1.00)
KLHL4	12 (8%)	143	0.00939 (1.00)	0.312 (1.00)	0.00618 (1.00)	0.0591 (1.00)	1 (1.00)	0.0246 (1.00)	0.0194 (1.00)	0.283 (1.00)	0.283 (1.00)
ROBO1	14 (9%)	141	0.128 (1.00)	0.107 (1.00)	0.0866 (1.00)	0.018 (1.00)	0.59 (1.00)	0.21 (1.00)	0.0863 (1.00)	1 (1.00)	0.386 (1.00)
GGT1	3 (2%)	152			0.317 (1.00)			0.483 (1.00)	0.665 (1.00)	1 (1.00)	1 (1.00)
PCDHB2	13 (8%)	142	0.0227 (1.00)	0.0327 (1.00)	0.0912 (1.00)	1 (1.00)	1 (1.00)	0.127 (1.00)	0.0255 (1.00)	1 (1.00)	0.336 (1.00)
POSTN	11 (7%)	144	0.302 (1.00)	0.674 (1.00)	0.0759 (1.00)	0.338 (1.00)	0.565 (1.00)	0.51 (1.00)	0.188 (1.00)	1 (1.00)	1 (1.00)
GRIK3	14 (9%)	141	0.405 (1.00)	0.169 (1.00)	0.476 (1.00)	0.518 (1.00)	0.618 (1.00)	0.277 (1.00)	0.697 (1.00)	1 (1.00)	1 (1.00)
LRRN3	9 (6%)	146	0.0213 (1.00)	0.224 (1.00)	0.288 (1.00)	0.0501 (1.00)	0.179 (1.00)	0.00294 (1.00)	0.0089 (1.00)	0.226 (1.00)	1 (1.00)
PRDM9	11 (7%)	144	0.002 (1.00)	0.674 (1.00)	0.129 (1.00)	0.226 (1.00)	0.867 (1.00)	0.0549 (1.00)	0.293 (1.00)	1 (1.00)	0.336 (1.00)
ADAM29	9 (6%)	146	0.498 (1.00)	0.387 (1.00)	0.268 (1.00)			0.811 (1.00)	0.413 (1.00)	1 (1.00)	1 (1.00)
KIAA1486	9 (6%)	146	0.817 (1.00)	0.8 (1.00)	0.469 (1.00)	0.604 (1.00)	1 (1.00)	0.783 (1.00)	0.662 (1.00)	1 (1.00)	0.255 (1.00)
PSG8	8 (5%)	147	0.425 (1.00)	0.204 (1.00)	0.197 (1.00)			0.78 (1.00)	1 (1.00)	0.226 (1.00)	0.102 (1.00)
NCKAP5	13 (8%)	142	0.143 (1.00)	0.0981 (1.00)	0.143 (1.00)	0.0103 (1.00)	1 (1.00)	0.306 (1.00)	0.00439 (1.00)	1 (1.00)	0.361 (1.00)
C8B	9 (6%)	146	0.23 (1.00)	0.233 (1.00)	0.853 (1.00)	0.338 (1.00)	1 (1.00)	0.603 (1.00)	0.413 (1.00)	1 (1.00)	1 (1.00)
CCDC160	5 (3%)	150	0.567 (1.00)	0.791 (1.00)	0.506 (1.00)			0.635 (1.00)	0.356 (1.00)	1 (1.00)	0.166 (1.00)
DCAF4L2	9 (6%)	146	0.0721 (1.00)	0.0173 (1.00)	0.232 (1.00)			0.122 (1.00)	0.00456 (1.00)	1 (1.00)	1 (1.00)
DKK2	5 (3%)	150	0.00788 (1.00)	0.101 (1.00)	0.506 (1.00)	0.405 (1.00)	0.446 (1.00)	0.0393 (1.00)	0.2 (1.00)	1 (1.00)	1 (1.00)
EPHA3	13 (8%)	142	0.00469 (1.00)	0.107 (1.00)	0.258 (1.00)	0.105 (1.00)	0.537 (1.00)	0.127 (1.00)	0.00942 (1.00)	1 (1.00)	0.361 (1.00)
ERBB4	14 (9%)	141	0.107 (1.00)	0.442 (1.00)	0.0538 (1.00)	1 (1.00)	0.521 (1.00)	0.0385 (1.00)	0.35 (1.00)	1 (1.00)	0.361 (1.00)
GUCY1A3	10 (6%)	145	0.129 (1.00)	0.125 (1.00)	0.227 (1.00)			0.0107 (1.00)	0.0196 (1.00)	1 (1.00)	0.283 (1.00)
IFT80	7 (5%)	148	0.567 (1.00)	0.274 (1.00)	0.135 (1.00)			0.377 (1.00)	0.258 (1.00)	0.197 (1.00)	1 (1.00)
INHBA	7 (5%)	148	0.112 (1.00)	0.401 (1.00)	0.312 (1.00)			0.368 (1.00)	0.0027 (1.00)	0.166 (1.00)	0.166 (1.00)
KLK2	3 (2%)	152	1 (1.00)	0.487 (1.00)	0.736 (1.00)			0.741 (1.00)	0.665 (1.00)	1 (1.00)
LPPR4	11 (7%)	144	0.105 (1.00)	0.0332 (1.00)	0.283 (1.00)	0.0673 (1.00)	0.757 (1.00)	0.388 (1.00)	0.121 (1.00)	1 (1.00)	1 (1.00)
OR7C1	6 (4%)	149	0.0289 (1.00)	0.145 (1.00)	0.744 (1.00)			0.621 (1.00)	0.258 (1.00)	1 (1.00)	0.197 (1.00)
SCN7A	12 (8%)	143	0.000451 (0.443)	0.0435 (1.00)	0.161 (1.00)	0.562 (1.00)	0.867 (1.00)	0.0124 (1.00)	0.0419 (1.00)	1 (1.00)	0.336 (1.00)
TGFBR2	7 (5%)	148	0.0252 (1.00)	0.213 (1.00)	0.0609 (1.00)			0.351 (1.00)	0.0027 (1.00)	0.197 (1.00)	0.197 (1.00)
TRPS1	13 (8%)	142	0.00661 (1.00)	0.33 (1.00)	0.000547 (0.536)			0.00352 (1.00)	0.00937 (1.00)	1 (1.00)	0.336 (1.00)
OR8J1	4 (3%)	151	0.425 (1.00)	0.371 (1.00)	0.619 (1.00)			0.123 (1.00)	0.753 (1.00)	1 (1.00)	0.103 (1.00)
RIMS2	12 (8%)	143	0.0121 (1.00)	0.123 (1.00)	0.0429 (1.00)	0.604 (1.00)	1 (1.00)	0.00837 (1.00)	0.0419 (1.00)	1 (1.00)	0.336 (1.00)
SFMBT2	12 (8%)	143	0.481 (1.00)	0.341 (1.00)	0.21 (1.00)	0.587 (1.00)	1 (1.00)	0.414 (1.00)	0.0194 (1.00)	1 (1.00)	0.361 (1.00)
IL18R1	8 (5%)	147	0.285 (1.00)	0.435 (1.00)	0.294 (1.00)	0.604 (1.00)	1 (1.00)	0.477 (1.00)	0.432 (1.00)	1 (1.00)	0.255 (1.00)
PCDH17	14 (9%)	141	0.0535 (1.00)	0.908 (1.00)	0.673 (1.00)	0.457 (1.00)	0.246 (1.00)	0.261 (1.00)	0.528 (1.00)	1 (1.00)	0.361 (1.00)
FLRT2	11 (7%)	144	0.695 (1.00)	0.908 (1.00)	0.367 (1.00)	0.091 (1.00)	1 (1.00)	0.562 (1.00)	1 (1.00)	1 (1.00)	0.283 (1.00)
PTEN	4 (3%)	151	0.132 (1.00)	0.306 (1.00)	0.132 (1.00)			0.0169 (1.00)	0.395 (1.00)	1 (1.00)	0.135 (1.00)
ZFHX4	17 (11%)	138	0.398 (1.00)	0.623 (1.00)	0.455 (1.00)	0.754 (1.00)	1 (1.00)	0.393 (1.00)	0.0964 (1.00)	1 (1.00)	0.0452 (1.00)
NRXN3	15 (10%)	140	0.00119 (1.00)	0.026 (1.00)	0.0506 (1.00)	0.911 (1.00)	0.267 (1.00)	0.0154 (1.00)	0.0542 (1.00)	1 (1.00)	0.386 (1.00)
LIFR	13 (8%)	142	0.17 (1.00)	0.806 (1.00)	0.355 (1.00)	0.78 (1.00)	0.565 (1.00)	0.498 (1.00)	0.249 (1.00)	1 (1.00)	0.0253 (1.00)
ZNF429	7 (5%)	148	0.364 (1.00)	0.599 (1.00)	0.887 (1.00)			0.0316 (1.00)	0.258 (1.00)	1 (1.00)	0.197 (1.00)
OR2M2	6 (4%)	149	0.364 (1.00)	0.735 (1.00)	0.574 (1.00)			0.741 (1.00)	0.815 (1.00)	1 (1.00)	0.166 (1.00)
SAT1	4 (3%)	151	0.00394 (1.00)	0.274 (1.00)	0.619 (1.00)	0.457 (1.00)	0.101 (1.00)	0.447 (1.00)	0.395 (1.00)	1 (1.00)	1 (1.00)
CDH18	10 (6%)	145	0.0216 (1.00)	0.256 (1.00)	0.0471 (1.00)	0.0857 (1.00)	0.537 (1.00)	0.532 (1.00)	0.182 (1.00)	1 (1.00)	0.283 (1.00)
P2RY10	6 (4%)	149	0.611 (1.00)	0.482 (1.00)	0.744 (1.00)			0.422 (1.00)	0.258 (1.00)	1 (1.00)	1 (1.00)
SYT16	6 (4%)	149	0.037 (1.00)	0.313 (1.00)	0.0596 (1.00)	0.081 (1.00)	0.565 (1.00)	0.0653 (1.00)	0.334 (1.00)	0.197 (1.00)	1 (1.00)
DKK4	4 (3%)	151	0.0704 (1.00)	0.274 (1.00)	0.188 (1.00)			0.264 (1.00)	0.395 (1.00)	1 (1.00)	1 (1.00)
NALCN	14 (9%)	141	0.00958 (1.00)	0.182 (1.00)	0.0129 (1.00)	1 (1.00)	0.82 (1.00)	0.0535 (1.00)	0.0255 (1.00)	1 (1.00)	0.361 (1.00)
SULT1C4	3 (2%)	152	0.0119 (1.00)	0.12 (1.00)	0.0684 (1.00)					1 (1.00)
UMOD	7 (5%)	148	0.0979 (1.00)	0.206 (1.00)	0.166 (1.00)	0.457 (1.00)	0.565 (1.00)	0.192 (1.00)	0.2 (1.00)	1 (1.00)	0.135 (1.00)
CPXCR1	6 (4%)	149	0.0704 (1.00)	0.404 (1.00)	0.574 (1.00)			0.833 (1.00)	0.258 (1.00)	0.197 (1.00)	0.0141 (1.00)
PDZRN4	12 (8%)	143	0.00568 (1.00)	0.0104 (1.00)	0.00593 (1.00)	0.604 (1.00)	1 (1.00)	0.000357 (0.351)	0.00111 (1.00)	0.31 (1.00)	0.31 (1.00)
USP17L2	7 (5%)	148	0.357 (1.00)	0.46 (1.00)	0.744 (1.00)	0.663 (1.00)	0.757 (1.00)	0.78 (1.00)	0.246 (1.00)	0.197 (1.00)	0.197 (1.00)
ESR1	11 (7%)	144	0.269 (1.00)	0.164 (1.00)	0.105 (1.00)	0.457 (1.00)	0.565 (1.00)	0.575 (1.00)	0.0397 (1.00)	1 (1.00)	0.283 (1.00)
FAM5C	10 (6%)	145	0.17 (1.00)	0.592 (1.00)	0.0471 (1.00)	0.0325 (1.00)	0.565 (1.00)	0.133 (1.00)	0.296 (1.00)	0.283 (1.00)	0.283 (1.00)
MIER3	10 (6%)	145	0.001 (0.971)	0.0246 (1.00)	0.00303 (1.00)	1 (1.00)	1 (1.00)	0.0155 (1.00)	0.0111 (1.00)	1 (1.00)	0.31 (1.00)
NLRP5	10 (6%)	145	0.0255 (1.00)	0.836 (1.00)	0.162 (1.00)			0.0231 (1.00)	0.793 (1.00)	1 (1.00)	0.255 (1.00)
OR6T1	6 (4%)	149	0.292 (1.00)	0.828 (1.00)	0.744 (1.00)			0.833 (1.00)	0.656 (1.00)	0.166 (1.00)	1 (1.00)
PCDH10	14 (9%)	141	0.146 (1.00)	0.235 (1.00)	0.237 (1.00)	0.647 (1.00)	1 (1.00)	0.0608 (1.00)	0.00998 (1.00)	1 (1.00)	0.361 (1.00)
PCDHB5	12 (8%)	143	0.0916 (1.00)	0.467 (1.00)	0.161 (1.00)	0.226 (1.00)	0.134 (1.00)	0.374 (1.00)	0.53 (1.00)	1 (1.00)	0.31 (1.00)
TRPC6	8 (5%)	147	0.11 (1.00)	0.947 (1.00)	0.35 (1.00)			0.254 (1.00)	0.361 (1.00)	1 (1.00)	0.197 (1.00)
RHOA	4 (3%)	151			0.619 (1.00)			0.447 (1.00)	0.0356 (1.00)	0.135 (1.00)	1 (1.00)
CYTL1	4 (3%)	151	0.381 (1.00)	0.338 (1.00)	0.619 (1.00)			0.209 (1.00)	1 (1.00)	1 (1.00)	0.135 (1.00)
CHRM2	8 (5%)	147	0.817 (1.00)	0.46 (1.00)	0.138 (1.00)	0.835 (1.00)	1 (1.00)	0.202 (1.00)	0.0125 (1.00)	0.226 (1.00)	0.226 (1.00)
GALNT14	9 (6%)	146	0.177 (1.00)	0.434 (1.00)	0.0807 (1.00)	0.0228 (1.00)	0.0412 (1.00)	0.0611 (1.00)	0.182 (1.00)	1 (1.00)	0.226 (1.00)
LRRIQ3	7 (5%)	148	0.635 (1.00)	0.633 (1.00)	0.47 (1.00)	0.113 (1.00)	0.565 (1.00)	0.862 (1.00)	0.585 (1.00)	1 (1.00)	0.226 (1.00)
NAALAD2	11 (7%)	144	0.0259 (1.00)	0.132 (1.00)	0.0127 (1.00)	0.604 (1.00)	0.246 (1.00)	0.0928 (1.00)	0.0397 (1.00)	1 (1.00)	0.283 (1.00)
PCDH11X	11 (7%)	144	0.055 (1.00)	0.674 (1.00)	0.129 (1.00)			0.0107 (1.00)	0.296 (1.00)	1 (1.00)	0.31 (1.00)
TFAP2D	5 (3%)	150	0.578 (1.00)	1 (1.00)	0.506 (1.00)	0.835 (1.00)	0.674 (1.00)	0.743 (1.00)	0.356 (1.00)	1 (1.00)	1 (1.00)
TNR	15 (10%)	140	0.0244 (1.00)	0.043 (1.00)	0.00125 (1.00)	0.663 (1.00)	1 (1.00)	0.0473 (1.00)	0.0108 (1.00)	1 (1.00)	1 (1.00)
CNTNAP4	10 (6%)	145	0.0354 (1.00)	0.687 (1.00)	0.0226 (1.00)	0.255 (1.00)	1 (1.00)	0.0413 (1.00)	0.0818 (1.00)	0.283 (1.00)	0.0325 (1.00)
DOCK2	16 (10%)	139	0.00217 (1.00)	0.0124 (1.00)	0.00754 (1.00)	0.336 (1.00)	0.438 (1.00)	0.00142 (1.00)	0.000566 (0.554)	1 (1.00)	0.433 (1.00)

'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 7.27e-06 (Fisher's exact test), Q value = 0.0073

Table S1. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	59	31	29	24
BRAF MUTATED	1	12	4	1
BRAF WILD-TYPE	58	19	25	23

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

'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 5.29e-07 (Fisher's exact test), Q value = 0.00053

Table S2. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	45	13	42
BRAF MUTATED	16	1	0	1
BRAF WILD-TYPE	27	44	13	41

Figure S2. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 8.5e-05 (Fisher's exact test), Q value = 0.085

Table S3. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	64	11	8
BRAF MUTATED	2	18	0	0
BRAF WILD-TYPE	68	46	11	8

Figure S3. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 7.22e-08 (Fisher's exact test), Q value = 7.3e-05

Table S4. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	47	34	18
BRAF MUTATED	1	18	1	0
BRAF WILD-TYPE	51	29	33	18

Figure S4. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.15e-07 (Fisher's exact test), Q value = 0.00012

Table S5. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	13	84
BRAF MUTATED	18	1	1
BRAF WILD-TYPE	36	12	83

Figure S5. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000215 (Fisher's exact test), Q value = 0.21

Table S6. Gene #4: 'KRAS MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	45	13	42
KRAS MUTATED	16	19	10	6
KRAS WILD-TYPE	27	26	3	36

Figure S6. Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 9.44e-08 (Fisher's exact test), Q value = 9.5e-05

Table S7. Gene #4: 'KRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	47	34	18
KRAS MUTATED	10	15	27	4
KRAS WILD-TYPE	42	32	7	14

Figure S7. Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.08e-09 (Fisher's exact test), Q value = 1.1e-06

Table S8. Gene #7: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	64	11	8
TP53 MUTATED	51	13	4	6
TP53 WILD-TYPE	19	51	7	2

Figure S8. Get High-res Image Gene #7: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'FAT4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000172 (Fisher's exact test), Q value = 0.17

Table S9. Gene #17: 'FAT4 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	64	11	8
FAT4 MUTATED	4	22	1	1
FAT4 WILD-TYPE	66	42	10	7

Figure S9. Get High-res Image Gene #17: 'FAT4 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'OR6N1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.13

Table S10. Gene #27: 'OR6N1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	59	31	29	24
OR6N1 MUTATED	0	6	0	0
OR6N1 WILD-TYPE	59	25	29	24

Figure S10. Get High-res Image Gene #27: 'OR6N1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'FLG MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.16

Table S11. Gene #48: 'FLG MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	59	31	29	24
FLG MUTATED	2	11	7	2
FLG WILD-TYPE	57	20	22	22

Figure S11. Get High-res Image Gene #48: 'FLG MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'FLG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.69e-05 (Fisher's exact test), Q value = 0.096

Table S12. Gene #48: 'FLG MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	13	84
FLG MUTATED	18	3	5
FLG WILD-TYPE	36	10	79

Figure S12. Get High-res Image Gene #48: 'FLG MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CHIERARCHICAL'

'OR51V1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000158 (Fisher's exact test), Q value = 0.16

Table S13. Gene #51: 'OR51V1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	13	84
OR51V1 MUTATED	9	0	0
OR51V1 WILD-TYPE	45	13	84

Figure S13. Get High-res Image Gene #51: 'OR51V1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CHIERARCHICAL'

'DNAH5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 8.23e-06 (Fisher's exact test), Q value = 0.0082

Table S14. Gene #60: 'DNAH5 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	59	31	29	24
DNAH5 MUTATED	5	14	8	0
DNAH5 WILD-TYPE	54	17	21	24

Figure S14. Get High-res Image Gene #60: 'DNAH5 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'CASP8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.04

Table S15. Gene #61: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	45	13	42
CASP8 MUTATED	9	0	0	0
CASP8 WILD-TYPE	34	45	13	42

Figure S15. Get High-res Image Gene #61: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.75e-05 (Fisher's exact test), Q value = 0.057

Table S16. Gene #61: 'CASP8 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	13	84
CASP8 MUTATED	10	0	0
CASP8 WILD-TYPE	44	13	84

Figure S16. Get High-res Image Gene #61: 'CASP8 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CHIERARCHICAL'

'ZC3H13 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.8e-05 (Fisher's exact test), Q value = 0.018

Table S17. Gene #82: 'ZC3H13 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	13	84
ZC3H13 MUTATED	15	0	2
ZC3H13 WILD-TYPE	39	13	82

Figure S17. Get High-res Image Gene #82: 'ZC3H13 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CHIERARCHICAL'

'TMEM132D MUTATION STATUS' versus 'MRNA_CNMF'

P value = 4.92e-05 (Fisher's exact test), Q value = 0.049

Table S18. Gene #89: 'TMEM132D MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	59	31	29	24
TMEM132D MUTATED	1	10	1	1
TMEM132D WILD-TYPE	58	21	28	23

Figure S18. Get High-res Image Gene #89: 'TMEM132D MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'SYNE1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.000178 (Fisher's exact test), Q value = 0.18

Table S19. Gene #110: 'SYNE1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	59	31	29	24
SYNE1 MUTATED	7	14	13	3
SYNE1 WILD-TYPE	52	17	16	21

Figure S19. Get High-res Image Gene #110: 'SYNE1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

Methods & Data

Input

Mutation data file = COAD-TP.mutsig.cluster.txt
Molecular subtypes file = COAD-TP.transferedmergedcluster.txt
Number of patients = 155
Number of significantly mutated genes = 120
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

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] 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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