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This article is part of the supplement: Proceedings of the Tenth Annual MCBIOS Conference

Open Access Proceedings

mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis

Cory B Giles12*, Reshmi Girija-Devi3*, Mikhail G Dozmorov1 and Jonathan D Wren12*

Author Affiliations

1 Oklahoma Medical Research Foundation, Oklahoma City, Arthritis and Clinical Immunology Research Program, 825 N.E. st, Oklahoma City, OK 73104-5005, USA

2 University of Oklahoma Health Sciences Center, Department of Biochemistry and Molecular Biology, 940 Stanton L. Young Blvd, OK 73104-5005, USA

3 Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India

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BMC Bioinformatics 2013, 14(Suppl 14):S17  doi:10.1186/1471-2105-14-S14-S17

Published: 9 October 2013

Abstract

Background

Experimentally validated co-expression correlations between miRNAs and genes are a valuable resource to corroborate observations about miRNA/mRNA changes after experimental perturbations, as well as compare miRNA target predictions with empirical observations. For example, when a given miRNA is transcribed, true targets of that miRNA should tend to have lower expression levels relative to when the miRNA is not expressed.

Methods

We processed publicly available human RNA-seq experiments obtained from NCBI's Sequence Read Archive (SRA) to identify miRNA-mRNA co-expression trends and summarized them in terms of their Pearson's Correlation Coefficient (PCC) and significance.

Results

We found that sequence-derived parameters from TargetScan and miRanda were predictive of co-expression, and that TargetScan- and miRanda-derived gene-miRNA pairs tend to have anti-correlated expression patterns in RNA-seq data compared to controls. We provide this data for download and as a web application available at http://wrenlab.org/mirCoX/ webcite.

Conclusion

This database of empirically established miRNA-mRNA transcriptional correlations will help to corroborate experimental observations and could be used to help refine and validate miRNA target predictions.