Correlation between miRseq expression and clinical features

Ovarian Serous Cystadenocarcinoma (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 miRseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1T43S0J

Overview

Introduction

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

Summary

Testing the association between 415 miRs and 7 clinical features across 453 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 2 clinical features related to at least one miRs.

8 miRs correlated to 'AGE'.

HSA-MIR-1269 , HSA-MIR-30D , HSA-MIR-767 , HSA-MIR-1234 , HSA-MIR-135A-1 , ...

1 miR correlated to 'RACE'.

HSA-MIR-1304

No miRs correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'ETHNICITY'.

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 miRs that are significantly associated with each clinical feature at P value < 0.05 and Q value < 0.3.

Clinical feature	Statistical test	Significant miRs	Associated with		Associated with
Time to Death	Cox regression test	N=0
AGE	Spearman correlation test	N=8	older	N=4	younger	N=4
PRIMARY SITE OF DISEASE	Kruskal-Wallis test	N=0
KARNOFSKY PERFORMANCE SCORE	Spearman correlation test	N=0
RADIATIONS RADIATION REGIMENINDICATION	Wilcoxon test	N=0
RACE	Kruskal-Wallis test	N=1
ETHNICITY	Wilcoxon test	N=0

Clinical variable #1: 'Time to Death'

No miR related to 'Time to Death'.

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


Time to Death	Duration (Months)	0.3-180.2 (median=30.1)
	censored	N = 198
	death	N = 252

	Significant markers	N = 0

Clinical variable #2: 'AGE'

8 miRs related to 'AGE'.

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


AGE	Mean (SD)	59.76 (12)
	Significant markers	N = 8
	pos. correlated	4
	neg. correlated	4

List of 8 miRs differentially expressed by 'AGE'

Table S3. Get Full Table List of 8 miRs significantly correlated to 'AGE' by Spearman correlation test

	SpearmanCorr	corrP	Q
HSA-MIR-1269	0.3263	1.7e-12	7.06e-10
HSA-MIR-30D	-0.2603	2.52e-08	1.04e-05
HSA-MIR-767	0.1997	5.628e-05	0.0232
HSA-MIR-1234	-0.1859	0.0001418	0.0584
HSA-MIR-135A-1	0.1857	0.0001502	0.0617
HSA-MIR-222	-0.1671	0.0003988	0.164
HSA-MIR-1908	0.1903	0.0005195	0.212
HSA-MIR-190	-0.2191	0.0005815	0.237

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

No miR related to 'PRIMARY.SITE.OF.DISEASE'.

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


PRIMARY.SITE.OF.DISEASE	Labels	N
	OMENTUM	2
	OVARY	450
	PERITONEUM OVARY	1

	Significant markers	N = 0

Clinical variable #4: 'KARNOFSKY.PERFORMANCE.SCORE'

No miR related to 'KARNOFSKY.PERFORMANCE.SCORE'.

Table S5. Basic characteristics of clinical feature: 'KARNOFSKY.PERFORMANCE.SCORE'


KARNOFSKY.PERFORMANCE.SCORE	Mean (SD)	75.31 (13)
	Score	N
	40	2
	60	17
	80	39
	100	6

	Significant markers	N = 0

Clinical variable #5: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

Table S6. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'


RADIATIONS.RADIATION.REGIMENINDICATION	Labels	N
	NO	3
	YES	450

	Significant markers	N = 0

Clinical variable #6: 'RACE'

One miR related to 'RACE'.

Table S7. Basic characteristics of clinical feature: 'RACE'


RACE	Labels	N
	AMERICAN INDIAN OR ALASKA NATIVE	2
	ASIAN	15
	BLACK OR AFRICAN AMERICAN	21
	WHITE	400

	Significant markers	N = 1

List of one miR differentially expressed by 'RACE'

Table S8. Get Full Table List of one miR differentially expressed by 'RACE'

	ANOVA_P	Q
HSA-MIR-1304	0.0004978	0.207

Clinical variable #7: 'ETHNICITY'

No miR related to 'ETHNICITY'.

Table S9. Basic characteristics of clinical feature: 'ETHNICITY'


ETHNICITY	Labels	N
	HISPANIC OR LATINO	8
	NOT HISPANIC OR LATINO	262

	Significant markers	N = 0

Methods & Data

Input

Expresson data file = OV-TP.miRseq_RPKM_log2.txt
Clinical data file = OV-TP.merged_data.txt
Number of patients = 453
Number of miRs = 415
Number of clinical features = 7

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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