Visualization of sRNA-mRNA Interaction Predictions

• Published in: 2016 20th International Conference Information Visualisation (IV) pp. 342 - 347
• Main Authors: Sansen, Joris, Thebault, Patricia, Dutour, Isabelle, Bourqui, Romain
• Format: Conference Proceeding Journal Article
• Language: English
• Published: IEEE 01-07-2016
• Subjects: Bacteria; Bioinformatics; Biological activity; biological data visualization; DNA; Electronics; Escherichia coli; Lists; overlapping clusters; Pipelines; Proteins; Ribonucleic acids; RNA; RNA interaction prediction; Translations; Visualization
• ISSN: 2375-0138
• DOI: 10.1109/IV.2016.14

The central dogma in molecular biology postulated that 'DNA makes RNA makes protein', however this dogma has been recently extended to integrate new biological activities involving small non-coding RNAs, called sRNAs. In particular, it has been shown that sRNAs regulate the production of proteins by interacting on mRNAs to regulate positively or negatively their translations. That regulation of the mRNA translation is done by forming a base-pairing between the RNAs sequences of bases. In silico methods have been proposed by the bioinformatics community toprovide a list of putative interactions to be experimentally validated. However, such approaches suffers from a poor specificity and therefore produce a large number of false predictions. In this paper, we present a new visualization technique for sRNA-mRNA interactions emphasizing theinvolved regions on the sRNA secondary structure drawing. Our approach also supports interactive exploration as the user can select and highlight interactions. We demonstrate the usefulness of our approach by a case study on E. coli bacteria performed by domain experts.