Correlation between miRseq expression and clinical features

Prostate Adenocarcinoma (Primary solid tumor)

22 February 2013 | analyses__2013_02_22

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/C1Q23XGV

Overview

Introduction

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

Summary

Testing the association between 487 genes and 2 clinical features across 146 samples, statistically thresholded by Q value < 0.05, 1 clinical feature related to at least one genes.

1 gene correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

HSA-MIR-449A

No genes correlated to 'AGE'

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
RADIATIONS RADIATION REGIMENINDICATION	t test	N=1	yes	N=1	no	N=0

Clinical variable #1: 'AGE'

No gene related to 'AGE'.

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


AGE	Mean (SD)	60.38 (7)
	Significant markers	N = 0

Clinical variable #2: 'RADIATIONS.RADIATION.REGIMENINDICATION'

One gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S2. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'


RADIATIONS.RADIATION.REGIMENINDICATION	Labels	N
	NO	5
	YES	141

	Significant markers	N = 1
	Higher in YES	1
	Higher in NO	0

List of one gene differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S3. Get Full Table List of one gene differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

	T(pos if higher in 'YES')	ttestP	Q	AUC
HSA-MIR-449A	4.27	7.692e-05	0.0338	0.6197

Figure S1. Get High-res Image As an example, this figure shows the association of HSA-MIR-449A to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 7.69e-05 with T-test analysis.

Methods & Data

Input

Expresson data file = PRAD-TP.miRseq_RPKM_log2.txt
Clinical data file = PRAD-TP.clin.merged.picked.txt
Number of patients = 146
Number of genes = 487
Number of clinical features = 2

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

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] 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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