Correlation between miRseq expression and clinical features

Liver Hepatocellular Carcinoma (Primary solid tumor)

23 September 2013 | analyses__2013_09_23

Maintainer Information

Citation Information

Maintained by Juok Cho (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between miRseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C179431J

Overview

Introduction

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

Summary

Testing the association between 551 genes and 8 clinical features across 114 samples, statistically thresholded by Q value < 0.05, 1 clinical feature related to at least one genes.

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

HSA-MIR-29B-1 , HSA-MIR-29B-2 , HSA-MIR-200C

No genes correlated to 'Time to Death', 'AGE', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', 'PATHOLOGY.M.STAGE', 'GENDER', and 'COMPLETENESS.OF.RESECTION'.

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
Time to Death	Cox regression test	N=0
AGE	Spearman correlation test	N=0
NEOPLASM DISEASESTAGE	ANOVA test	N=0
PATHOLOGY T STAGE	Spearman correlation test	N=0
PATHOLOGY N STAGE	t test	N=3	class1	N=2	class0	N=1
PATHOLOGY M STAGE	ANOVA test	N=0
GENDER	t test	N=0
COMPLETENESS OF RESECTION	ANOVA test	N=0

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)	0-113 (median=15.7)
	censored	N = 60
	death	N = 50

	Significant markers	N = 0

Clinical variable #2: 'AGE'

No gene related to 'AGE'.

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


AGE	Mean (SD)	61.4 (14)
	Significant markers	N = 0

Clinical variable #3: 'NEOPLASM.DISEASESTAGE'

No gene related to 'NEOPLASM.DISEASESTAGE'.

Table S3. Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'


NEOPLASM.DISEASESTAGE	Labels	N
	STAGE I	42
	STAGE II	24
	STAGE III	2
	STAGE IIIA	25
	STAGE IIIB	3
	STAGE IIIC	5
	STAGE IV	1
	STAGE IVA	1
	STAGE IVB	1

	Significant markers	N = 0

Clinical variable #4: 'PATHOLOGY.T.STAGE'

No gene related to 'PATHOLOGY.T.STAGE'.

Table S4. Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'


PATHOLOGY.T.STAGE	Mean (SD)	2.03 (0.98)
		N
	1	45
	2	27
	3	34
	4	7

	Significant markers	N = 0

Clinical variable #5: 'PATHOLOGY.N.STAGE'

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

Table S5. Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'


PATHOLOGY.N.STAGE	Labels	N
	class0	73
	class1	3

	Significant markers	N = 3
	Higher in class1	2
	Higher in class0	1

List of 3 genes differentially expressed by 'PATHOLOGY.N.STAGE'

Table S6. Get Full Table List of 3 genes differentially expressed by 'PATHOLOGY.N.STAGE'

	T(pos if higher in 'class1')	ttestP	Q	AUC
HSA-MIR-29B-1	5.42	7.837e-07	0.000284	0.7489
HSA-MIR-29B-2	4.7	2.868e-05	0.0104	0.7306
HSA-MIR-200C	-4.51	3.408e-05	0.0123	0.726

Figure S1. Get High-res Image As an example, this figure shows the association of HSA-MIR-29B-1 to 'PATHOLOGY.N.STAGE'. P value = 7.84e-07 with T-test analysis.

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

No gene related to 'PATHOLOGY.M.STAGE'.

Table S7. Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'


PATHOLOGY.M.STAGE	Labels	N
	M0	89
	M1	2
	MX	23

	Significant markers	N = 0

Clinical variable #7: 'GENDER'

No gene related to 'GENDER'.

Table S8. Basic characteristics of clinical feature: 'GENDER'


GENDER	Labels	N
	FEMALE	43
	MALE	71

	Significant markers	N = 0

Clinical variable #8: 'COMPLETENESS.OF.RESECTION'

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

Table S9. Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'


COMPLETENESS.OF.RESECTION	Labels	N
	R0	89
	R1	10
	R2	1
	RX	9

	Significant markers	N = 0

Methods & Data

Input

Expresson data file = LIHC-TP.miRseq_RPKM_log2.txt
Clinical data file = LIHC-TP.clin.merged.picked.txt
Number of patients = 114
Number of genes = 551
Number of clinical features = 8

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

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

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

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

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

[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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