Correlation between mRNAseq expression and clinical features

Colorectal Adenocarcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

Maintained by Juok Cho (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between mRNAseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1348J75

Overview

Introduction

This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features.

Summary

Testing the association between 18035 genes and 13 clinical features across 601 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 11 clinical features related to at least one genes.

37 genes correlated to 'AGE'.

MTERF|7978 , AMH|268 , MGA|23269 , CNTD2|79935 , MRE11A|4361 , ...

184 genes correlated to 'PRIMARY.SITE.OF.DISEASE'.

HOXB13|10481 , ZNF528|84436 , ELAVL2|1993 , ZNF530|348327 , ZNF662|389114 , ...

105 genes correlated to 'NEOPLASM.DISEASESTAGE'.

RGL2|5863 , C5ORF23|79614 , C2CD4A|145741 , GSR|2936 , BEND3|57673 , ...

188 genes correlated to 'PATHOLOGY.T.STAGE'.

SCG2|7857 , C5ORF23|79614 , SPP1|6696 , SOX11|6664 , CSRP2|1466 , ...

353 genes correlated to 'PATHOLOGY.N.STAGE'.

GSR|2936 , TEAD3|7005 , RGL2|5863 , C5ORF23|79614 , AGPAT5|55326 , ...

514 genes correlated to 'PATHOLOGY.M.STAGE'.

FUNDC2P2|388965 , POTEE|445582 , MCART2|147407 , LOC344967|344967 , SPIN2A|54466 , ...

10 genes correlated to 'GENDER'.

CYORF15A|246126 , CYORF15B|84663 , HDHD1A|8226 , NCRNA00183|554203 , SPESP1|246777 , ...

1380 genes correlated to 'HISTOLOGICAL.TYPE'.

PLAGL2|5326 , POFUT1|23509 , SLC19A3|80704 , SLC5A6|8884 , MUC2|4583 , ...

628 genes correlated to 'COMPLETENESS.OF.RESECTION'.

RRN3P2|653390 , LOC150776|150776 , PMS2CL|441194 , POLR2J4|84820 , SCXB|642658 , ...

237 genes correlated to 'NUMBER.OF.LYMPH.NODES'.

GSR|2936 , TEAD3|7005 , CASP1|834 , C5ORF23|79614 , NPR3|4883 , ...

19 genes correlated to 'RACE'.

ULK4|54986 , LOC441455|441455 , C14ORF167|55449 , NOTCH2NL|388677 , PPIL3|53938 , ...

No genes correlated to 'Time to Death', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Results

Overview of the results

Complete statistical result table is provided in Supplement Table 1

Table 1. Get Full Table This table shows the clinical features, statistical methods used, and the number of genes that are significantly associated with each clinical feature at P value < 0.05 and Q value < 0.3.

Clinical feature	Statistical test	Significant genes	Associated with		Associated with
Time to Death	Cox regression test	N=0
AGE	Spearman correlation test	N=37	older	N=13	younger	N=24
PRIMARY SITE OF DISEASE	Wilcoxon test	N=184	rectum	N=184	colon	N=0
NEOPLASM DISEASESTAGE	Kruskal-Wallis test	N=105
PATHOLOGY T STAGE	Spearman correlation test	N=188	higher stage	N=172	lower stage	N=16
PATHOLOGY N STAGE	Spearman correlation test	N=353	higher stage	N=240	lower stage	N=113
PATHOLOGY M STAGE	Kruskal-Wallis test	N=514
GENDER	Wilcoxon test	N=10	male	N=10	female	N=0
HISTOLOGICAL TYPE	Kruskal-Wallis test	N=1380
RADIATIONS RADIATION REGIMENINDICATION	Wilcoxon test	N=0
COMPLETENESS OF RESECTION	Kruskal-Wallis test	N=628
NUMBER OF LYMPH NODES	Spearman correlation test	N=237	higher number.of.lymph.nodes	N=153	lower number.of.lymph.nodes	N=84
RACE	Kruskal-Wallis test	N=19

Clinical variable #1: 'Time to Death'

No gene related to 'Time to Death'.

Table S1. Basic characteristics of clinical feature: 'Time to Death'


Time to Death	Duration (Months)	0.1-140.4 (median=18)
	censored	N = 463
	death	N = 109

	Significant markers	N = 0

Clinical variable #2: 'AGE'

37 genes related to 'AGE'.

Table S2. Basic characteristics of clinical feature: 'AGE'


AGE	Mean (SD)	66.49 (13)
	Significant markers	N = 37
	pos. correlated	13
	neg. correlated	24

List of top 10 genes differentially expressed by 'AGE'

Table S3. Get Full Table List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test

	SpearmanCorr	corrP	Q
MTERF\|7978	-0.2408	2.518e-09	4.54e-05
AMH\|268	0.2328	1.444e-08	0.00026
MGA\|23269	-0.2251	2.493e-08	0.00045
CNTD2\|79935	0.2088	2.563e-07	0.00462
MRE11A\|4361	-0.2008	7.278e-07	0.0131
TGFBR2\|7048	-0.197	1.155e-06	0.0208
ZNF134\|7693	-0.1958	1.404e-06	0.0253
LOC154761\|154761	0.1955	1.427e-06	0.0257
ZNF518B\|85460	-0.1911	2.526e-06	0.0455
ZNF75A\|7627	-0.1882	3.572e-06	0.0644

Clinical variable #3: 'PRIMARY.SITE.OF.DISEASE'

184 genes related to 'PRIMARY.SITE.OF.DISEASE'.

Table S4. Basic characteristics of clinical feature: 'PRIMARY.SITE.OF.DISEASE'


PRIMARY.SITE.OF.DISEASE	Labels	N
	COLON	437
	RECTUM	160

	Significant markers	N = 184
	Higher in RECTUM	184
	Higher in COLON	0

List of top 10 genes differentially expressed by 'PRIMARY.SITE.OF.DISEASE'

Table S5. Get Full Table List of top 10 genes differentially expressed by 'PRIMARY.SITE.OF.DISEASE'

	W(pos if higher in 'RECTUM')	wilcoxontestP	Q	AUC
HOXB13\|10481	48933	4.587e-14	8.27e-10	0.7014
ZNF528\|84436	46390.5	4.555e-10	8.21e-06	0.6665
ELAVL2\|1993	37834	6.841e-10	1.23e-05	0.6712
ZNF530\|348327	46262	7.067e-10	1.27e-05	0.6647
ZNF662\|389114	46004	8.447e-10	1.52e-05	0.664
HOXC4\|3221	18471.5	1.376e-09	2.48e-05	0.6718
HOXC6\|3223	15520	1.845e-09	3.33e-05	0.6791
ZNF813\|126017	45746	2.01e-09	3.62e-05	0.6603
ZNF141\|7700	45516	3.07e-09	5.53e-05	0.6585
ELAC1\|55520	24090	5.779e-09	0.000104	0.6555

Clinical variable #4: 'NEOPLASM.DISEASESTAGE'

105 genes related to 'NEOPLASM.DISEASESTAGE'.

Table S6. Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'


NEOPLASM.DISEASESTAGE	Labels	N
	STAGE I	102
	STAGE IA	1
	STAGE II	35
	STAGE IIA	171
	STAGE IIB	11
	STAGE IIC	3
	STAGE III	27
	STAGE IIIA	21
	STAGE IIIB	78
	STAGE IIIC	52
	STAGE IV	59
	STAGE IVA	26
	STAGE IVB	1

	Significant markers	N = 105

List of top 10 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

Table S7. Get Full Table List of top 10 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

	ANOVA_P	Q
RGL2\|5863	2.816e-09	5.08e-05
C5ORF23\|79614	5.722e-09	0.000103
C2CD4A\|145741	1.46e-08	0.000263
GSR\|2936	2.41e-08	0.000435
BEND3\|57673	4.06e-08	0.000732
C13ORF15\|28984	5.17e-08	0.000932
NPR3\|4883	1.046e-07	0.00189
IRF1\|3659	1.451e-07	0.00262
CDRT1\|374286	2.159e-07	0.00389
LAP3\|51056	2.43e-07	0.00438

Clinical variable #5: 'PATHOLOGY.T.STAGE'

188 genes related to 'PATHOLOGY.T.STAGE'.

Table S8. Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'


PATHOLOGY.T.STAGE	Mean (SD)	2.87 (0.63)
		N
	1	20
	2	105
	3	409
	4	65

	Significant markers	N = 188
	pos. correlated	172
	neg. correlated	16

List of top 10 genes differentially expressed by 'PATHOLOGY.T.STAGE'

Table S9. Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

	SpearmanCorr	corrP	Q
SCG2\|7857	0.2513	5.226e-10	9.43e-06
C5ORF23\|79614	0.2503	1.193e-09	2.15e-05
SPP1\|6696	0.2364	4.738e-09	8.54e-05
SOX11\|6664	0.239	5.586e-09	0.000101
CSRP2\|1466	0.233	7.888e-09	0.000142
OLR1\|4973	0.234	8.301e-09	0.00015
HTR2B\|3357	0.2384	8.594e-09	0.000155
LOC100126784\|100126784	0.2456	9.854e-09	0.000178
NALCN\|259232	0.244	1.393e-08	0.000251
S1PR3\|1903	0.2248	2.662e-08	0.00048

Clinical variable #6: 'PATHOLOGY.N.STAGE'

353 genes related to 'PATHOLOGY.N.STAGE'.

Table S10. Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'


PATHOLOGY.N.STAGE	Mean (SD)	0.61 (0.78)
		N
	0	341
	1	147
	2	109

	Significant markers	N = 353
	pos. correlated	240
	neg. correlated	113

List of top 10 genes differentially expressed by 'PATHOLOGY.N.STAGE'

Table S11. Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.N.STAGE' by Spearman correlation test

	SpearmanCorr	corrP	Q
GSR\|2936	-0.2831	1.838e-12	3.32e-08
TEAD3\|7005	0.2792	3.77e-12	6.8e-08
RGL2\|5863	0.2546	2.735e-10	4.93e-06
C5ORF23\|79614	0.2568	4.555e-10	8.21e-06
AGPAT5\|55326	-0.2512	4.818e-10	8.69e-06
COQ2\|27235	-0.2485	7.433e-10	1.34e-05
NAT1\|9	-0.2482	7.782e-10	1.4e-05
CASP1\|834	-0.2481	7.958e-10	1.43e-05
TCHH\|7062	0.2466	2.831e-09	5.1e-05
NPR3\|4883	0.2582	3.292e-09	5.93e-05

Clinical variable #7: 'PATHOLOGY.M.STAGE'

514 genes related to 'PATHOLOGY.M.STAGE'.

Table S12. Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'


PATHOLOGY.M.STAGE	Labels	N
	M0	449
	M1	71
	M1A	10
	M1B	1
	MX	61

	Significant markers	N = 514

List of top 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'

Table S13. Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'

	ANOVA_P	Q
FUNDC2P2\|388965	3.695e-12	6.66e-08
POTEE\|445582	7.385e-12	1.33e-07
MCART2\|147407	1.952e-11	3.52e-07
LOC344967\|344967	2.104e-11	3.79e-07
SPIN2A\|54466	2.692e-11	4.85e-07
NBPF15\|284565	2.797e-11	5.04e-07
EDARADD\|128178	3.505e-11	6.32e-07
UBE2NL\|389898	6.395e-11	1.15e-06
C14ORF19\|280655	1.225e-10	2.21e-06
PPIAL4D\|645142	1.562e-10	2.82e-06

Clinical variable #8: 'GENDER'

10 genes related to 'GENDER'.

Table S14. Basic characteristics of clinical feature: 'GENDER'


GENDER	Labels	N
	FEMALE	279
	MALE	322

	Significant markers	N = 10
	Higher in MALE	10
	Higher in FEMALE	0

List of 10 genes differentially expressed by 'GENDER'

Table S15. Get Full Table List of 10 genes differentially expressed by 'GENDER'. 42 significant gene(s) located in sex chromosomes is(are) filtered out.

	W(pos if higher in 'MALE')	wilcoxontestP	Q	AUC
CYORF15A\|246126	23504	6.095e-39	1.1e-34	0.9864
CYORF15B\|84663	20075	7.111e-34	1.28e-29	0.9802
HDHD1A\|8226	20735	4.609e-30	8.31e-26	0.7692
NCRNA00183\|554203	24022	7.335e-23	1.32e-18	0.7326
SPESP1\|246777	47584	6.593e-08	0.00119	0.6337
FRG1B\|284802	56159	7.274e-08	0.00131	0.6274
CD207\|50489	30189	6.212e-07	0.0112	0.6214
C2ORF84\|653140	30515.5	6.245e-06	0.112	0.6249
ZNF578\|147660	34946.5	6.339e-06	0.114	0.607
CXORF38\|159013	35450	8.193e-06	0.147	0.6054

Clinical variable #9: 'HISTOLOGICAL.TYPE'

1380 genes related to 'HISTOLOGICAL.TYPE'.

Table S16. Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'


HISTOLOGICAL.TYPE	Labels	N
	COLON ADENOCARCINOMA	379
	COLON MUCINOUS ADENOCARCINOMA	57
	RECTAL ADENOCARCINOMA	144
	RECTAL MUCINOUS ADENOCARCINOMA	13

	Significant markers	N = 1380

List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S17. Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

	ANOVA_P	Q
PLAGL2\|5326	8.155e-20	1.47e-15
POFUT1\|23509	9.17e-19	1.65e-14
SLC19A3\|80704	6.011e-18	1.08e-13
SLC5A6\|8884	3.367e-17	6.07e-13
MUC2\|4583	3.633e-17	6.55e-13
SNHG11\|128439	5.008e-17	9.03e-13
ACTR5\|79913	6.127e-17	1.1e-12
AQP3\|360	1.893e-16	3.41e-12
TM9SF4\|9777	2.135e-16	3.85e-12
HNF4A\|3172	2.204e-16	3.97e-12

Clinical variable #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S18. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'


RADIATIONS.RADIATION.REGIMENINDICATION	Labels	N
	NO	9
	YES	592

	Significant markers	N = 0

Clinical variable #11: 'COMPLETENESS.OF.RESECTION'

628 genes related to 'COMPLETENESS.OF.RESECTION'.

Table S19. Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'


COMPLETENESS.OF.RESECTION	Labels	N
	R0	434
	R1	5
	R2	35
	RX	28

	Significant markers	N = 628

List of top 10 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

Table S20. Get Full Table List of top 10 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

	ANOVA_P	Q
RRN3P2\|653390	8.363e-12	1.51e-07
LOC150776\|150776	1.26e-11	2.27e-07
PMS2CL\|441194	1.774e-11	3.2e-07
POLR2J4\|84820	3.249e-11	5.86e-07
SCXB\|642658	4.247e-11	7.66e-07
GUSBL2\|375513	6.601e-11	1.19e-06
NSUN5P1\|155400	6.66e-11	1.2e-06
AGAP11\|119385	7.776e-11	1.4e-06
CCDC85B\|11007	8.55e-11	1.54e-06
PMS2L2\|5380	9.867e-11	1.78e-06

Clinical variable #12: 'NUMBER.OF.LYMPH.NODES'

237 genes related to 'NUMBER.OF.LYMPH.NODES'.

Table S21. Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'


NUMBER.OF.LYMPH.NODES	Mean (SD)	2.2 (4.7)
	Significant markers	N = 237
	pos. correlated	153
	neg. correlated	84

List of top 10 genes differentially expressed by 'NUMBER.OF.LYMPH.NODES'

Table S22. Get Full Table List of top 10 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

	SpearmanCorr	corrP	Q
GSR\|2936	-0.277	1.971e-11	3.56e-07
TEAD3\|7005	0.2622	2.378e-10	4.29e-06
CASP1\|834	-0.2595	3.654e-10	6.59e-06
C5ORF23\|79614	0.261	7.14e-10	1.29e-05
NPR3\|4883	0.2689	1.977e-09	3.57e-05
SHC1\|6464	0.2479	2.252e-09	4.06e-05
C2CD4A\|145741	-0.2467	2.714e-09	4.89e-05
CXCL2\|2920	-0.2467	2.722e-09	4.91e-05
RGL2\|5863	0.2426	4.988e-09	8.99e-05
AGPAT5\|55326	-0.2417	5.711e-09	0.000103

Clinical variable #13: 'RACE'

19 genes related to 'RACE'.

Table S23. Basic characteristics of clinical feature: 'RACE'


RACE	Labels	N
	AMERICAN INDIAN OR ALASKA NATIVE	1
	ASIAN	12
	BLACK OR AFRICAN AMERICAN	47
	WHITE	294

	Significant markers	N = 19

List of top 10 genes differentially expressed by 'RACE'

Table S24. Get Full Table List of top 10 genes differentially expressed by 'RACE'

	ANOVA_P	Q
ULK4\|54986	5.725e-11	1.03e-06
LOC441455\|441455	1.14e-10	2.06e-06
C14ORF167\|55449	1.419e-10	2.56e-06
NOTCH2NL\|388677	1.461e-09	2.63e-05
PPIL3\|53938	1.185e-08	0.000214
CROCCL1\|84809	3.382e-08	0.00061
CYP3A5\|1577	5.327e-08	0.00096
SPDYE1\|285955	4.084e-07	0.00736
RPS26\|6231	9.27e-07	0.0167
LOC90784\|90784	1.166e-06	0.021

Methods & Data

Input

Expresson data file = COADREAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
Clinical data file = COADREAD-TP.merged_data.txt
Number of patients = 601
Number of genes = 18035
Number of clinical features = 13

Survival analysis

For survival clinical features, Wald's test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values using the 'coxph' function in R. Kaplan-Meier survival curves were plot using the four quartile subgroups of patients based on expression levels

Correlation analysis

For continuous numerical clinical features, Spearman's rank correlation coefficients (Spearman 1904) and two-tailed P values were estimated using 'cor.test' function in R

Student's t-test analysis

For two-class clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the log2-expression levels between the two clinical classes using 't.test' function in R

ANOVA analysis

For multi-class clinical features (ordinal or nominal), one-way analysis of variance (Howell 2002) was applied to compare the log2-expression levels between different clinical classes using 'anova' 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] Andersen and Gill, Cox's regression model for counting processes, a large sample study, Annals of Statistics 10(4):1100-1120 (1982)

[2] Spearman, C, The proof and measurement of association between two things, Amer. J. Psychol 15:72-101 (1904)

[3] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)

[4] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)

[5] 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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