Correlation between mRNAseq expression and clinical features

Rectum Adenocarcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_23

Maintainer Information

Citation Information

Maintained by Juok Cho (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between mRNAseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1RR1W9N

Overview

Introduction

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

Summary

Testing the association between 18106 genes and 8 clinical features across 51 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one genes.

14 genes correlated to 'GENDER'.

DDX3Y|8653 , ZFY|7544 , XIST|7503 , EIF1AY|9086 , PRKY|5616 , ...

47 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

GUSBL2|375513 , TTC15|51112 , GNG3|2785 , RMND5B|64777 , ZNF608|57507 , ...

2 genes correlated to 'NEOPLASM.DISEASESTAGE'.

METT11D1|64745 , UBE2E3|10477

No genes correlated to 'AGE', 'DISTANT.METASTASIS', 'LYMPH.NODE.METASTASIS', 'COMPLETENESS.OF.RESECTION', and 'NUMBER.OF.LYMPH.NODES'.

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 Q value < 0.05.

Clinical feature	Statistical test	Significant genes	Associated with		Associated with
AGE	Spearman correlation test	N=0
GENDER	t test	N=14	male	N=12	female	N=2
RADIATIONS RADIATION REGIMENINDICATION	t test	N=47	yes	N=15	no	N=32
DISTANT METASTASIS	ANOVA test	N=0
LYMPH NODE METASTASIS	ANOVA test	N=0
COMPLETENESS OF RESECTION	ANOVA test	N=0
NUMBER OF LYMPH NODES	Spearman correlation test	N=0
NEOPLASM DISEASESTAGE	ANOVA test	N=2

Clinical variable #1: 'AGE'

No gene related to 'AGE'.

Table S1. Basic characteristics of clinical feature: 'AGE'


AGE	Mean (SD)	63.33 (12)
	Significant markers	N = 0

Clinical variable #2: 'GENDER'

14 genes related to 'GENDER'.

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


GENDER	Labels	N
	FEMALE	23
	MALE	28

	Significant markers	N = 14
	Higher in MALE	12
	Higher in FEMALE	2

List of top 10 genes differentially expressed by 'GENDER'

Table S3. Get Full Table List of top 10 genes differentially expressed by 'GENDER'

	T(pos if higher in 'MALE')	ttestP	Q	AUC
DDX3Y\|8653	31.09	9.353e-26	1.69e-21	1
ZFY\|7544	26.85	3.725e-25	6.74e-21	1
XIST\|7503	-19.94	1.177e-24	2.13e-20	1
EIF1AY\|9086	24.06	7.095e-22	1.28e-17	1
PRKY\|5616	15.42	6.024e-20	1.09e-15	1
USP9Y\|8287	22.78	1.041e-18	1.88e-14	1
CYORF15A\|246126	19.49	1.387e-18	2.51e-14	1
KDM5D\|8284	27.37	5.082e-18	9.19e-14	1
RPS4Y1\|6192	17.83	9.967e-17	1.8e-12	1
CYORF15B\|84663	15.97	8.844e-15	1.6e-10	1

Figure S1. Get High-res Image As an example, this figure shows the association of DDX3Y|8653 to 'GENDER'. P value = 9.35e-26 with T-test analysis.

Clinical variable #3: 'RADIATIONS.RADIATION.REGIMENINDICATION'

47 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S4. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'


RADIATIONS.RADIATION.REGIMENINDICATION	Labels	N
	NO	3
	YES	48

	Significant markers	N = 47
	Higher in YES	15
	Higher in NO	32

List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S5. Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

	T(pos if higher in 'YES')	ttestP	Q	AUC
GUSBL2\|375513	-9.35	2.16e-12	3.57e-08	0.8819
TTC15\|51112	8.72	1.792e-11	2.96e-07	0.9028
GNG3\|2785	-8.59	3.078e-11	5.09e-07	0.8958
RMND5B\|64777	8.67	1.021e-10	1.69e-06	0.9306
ZNF608\|57507	8.54	2.098e-10	3.47e-06	0.8958
PAK1IP1\|55003	-7.92	5.672e-10	9.38e-06	0.9236
DDX19A\|55308	-7.64	7.938e-10	1.31e-05	0.8681
TRA2B\|6434	-7.76	2.197e-09	3.63e-05	0.8889
WASH2P\|375260	-7.16	3.865e-09	6.39e-05	0.8542
TMEM117\|84216	-7.15	4.477e-09	7.4e-05	0.8681

Figure S2. Get High-res Image As an example, this figure shows the association of GUSBL2|375513 to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 2.16e-12 with T-test analysis.

Clinical variable #4: 'DISTANT.METASTASIS'

No gene related to 'DISTANT.METASTASIS'.

Table S6. Basic characteristics of clinical feature: 'DISTANT.METASTASIS'


DISTANT.METASTASIS	Labels	N
	M0	37
	M1	4
	M1A	1
	MX	9

	Significant markers	N = 0

Clinical variable #5: 'LYMPH.NODE.METASTASIS'

No gene related to 'LYMPH.NODE.METASTASIS'.

Table S7. Basic characteristics of clinical feature: 'LYMPH.NODE.METASTASIS'


LYMPH.NODE.METASTASIS	Labels	N
	N0	26
	N1	6
	N1A	1
	N1B	3
	N2	8
	N2B	5
	NX	2

	Significant markers	N = 0

Clinical variable #6: 'COMPLETENESS.OF.RESECTION'

No gene related to 'COMPLETENESS.OF.RESECTION'.

Table S8. Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'


COMPLETENESS.OF.RESECTION	Labels	N
	R0	35
	R1	1
	RX	3

	Significant markers	N = 0

Clinical variable #7: 'NUMBER.OF.LYMPH.NODES'

No gene related to 'NUMBER.OF.LYMPH.NODES'.

Table S9. Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'


NUMBER.OF.LYMPH.NODES	Mean (SD)	3.18 (5.9)
	Significant markers	N = 0

Clinical variable #8: 'NEOPLASM.DISEASESTAGE'

2 genes related to 'NEOPLASM.DISEASESTAGE'.

Table S10. Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'


NEOPLASM.DISEASESTAGE	Labels	N
	STAGE I	11
	STAGE II	2
	STAGE IIA	10
	STAGE IIB	1
	STAGE IIC	1
	STAGE IIIA	4
	STAGE IIIB	5
	STAGE IIIC	7
	STAGE IV	2
	STAGE IVA	5

	Significant markers	N = 2

List of 2 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

Table S11. Get Full Table List of 2 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

	ANOVA_P	Q
METT11D1\|64745	5.441e-07	0.00985
UBE2E3\|10477	8.896e-07	0.0161

Figure S3. Get High-res Image As an example, this figure shows the association of METT11D1|64745 to 'NEOPLASM.DISEASESTAGE'. P value = 5.44e-07 with ANOVA analysis.

Methods & Data

Input

Expresson data file = READ-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
Clinical data file = READ-TP.clin.merged.picked.txt
Number of patients = 51
Number of genes = 18106
Number of clinical features = 8

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

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

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

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

[4] 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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