Journal Article


Raymond L Stallings
Rogier Versteeg
Jan Koster
Karen M Watters
Raquel Domingo-Fernandez
Isabella M Bray
Marta Terrile
Kenneth Bryan



humans rna messenger micrornas gene expression regulation cluster analysis computer graphics models genetic software genetics metabolism immune system classification gene expression profiling neuroblastoma

Discovery and visualization of miRNA-mRNA functional modules within integrated data using bicluster analysis. (2013)

Abstract MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression at a post-transcriptional level. An miRNA may target many messenger RNA (mRNA) transcripts, and each transcript may be targeted by multiple miRNAs. Our understanding of miRNA regulation is evolving to consider modules of miRNAs that regulate groups of functionally related mRNAs. Here we expand the model of miRNA functional modules and use it to guide the integration of miRNA and mRNA expression and target prediction data. We present evidence of cooperativity between miRNA classes within this integrated miRNA-mRNA association matrix. We then apply bicluster analysis to uncover miRNA functional modules within this integrated data set and develop a novel application to visualize and query these results. We show that this wholly unsupervised approach can discover a network of miRNA-mRNA modules that are enriched for both biological processes and miRNA classes. We apply this method to investigate the interplay of miRNAs and mRNAs in integrated data sets derived from neuroblastoma and human immune cells. This study is the first to apply the technique of biclustering to model functional modules within an integrated miRNA-mRNA association matrix. Results provide evidence of an extensive modular miRNA functional network and enable characterization of miRNA function and dysregulation in disease.
Collections Ireland -> Royal College of Surgeons in Ireland -> PubMed

Full list of authors on original publication

Raymond L Stallings, Rogier Versteeg, Jan Koster, Karen M Watters, Raquel Domingo-Fernandez, Isabella M Bray, Marta Terrile, Kenneth Bryan

Experts in our system

Raymond L Stallings
Royal College of Surgeons in Ireland
Total Publications: 59
Isabella Bray
Royal College of Surgeons in Ireland
Total Publications: 35
Kenneth Bryan
Royal College of Surgeons in Ireland
Total Publications: 36