This article is part of the supplement: Proceedings of the Tenth Annual MCBIOS Conference
mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis
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
BMC Bioinformatics 2013, 14(Suppl 14):S17 doi:10.1186/1471-2105-14-S14-S17Published: 9 October 2013
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.
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.
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.
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.