Combing the Hairball: Improving Visualization of miRNA–Target Interaction Networks
The visualization of regulatory networks is becoming increasingly important in order to understand molecular mechanisms and diseases. MicroRNAs (miRNAs) are small noncoding RNAs (ncRNAs) responsible of the post-transcriptional regulation of messenger RNAs (mRNAs) and other ncRNAs. MiRNAs are involved in numerous biological processes including development, cell proliferation, and apoptosis. They are also key molecules in major complex diseases such as cancer and cardiovascular diseases. A single miRNA can regulate many targets, making the analysis and visualization of these complex networks challenging. Here, we present standard and advanced visualization approaches to represent networks with a special focus on miRNA–target interactions.
Key wordsMicroRNAs Noncoding RNAs Visualization Regulatory networks Target prediction
The authors would like to acknowledge funding from the Novo Nordisk Foundation (grant agreement NNF14CC0001).
- 10.Nazarov PV, Reinsbach SE, Muller A, Nicot N, Philippidou D, Vallar L, Kreis S (2013) Interplay of microRNAs, transcription factors and target genes: linking dynamic expression changes to function. Nucleic Acids Res 41:2817–2831. https://doi.org/10.1093/nar/gks1471CrossRefPubMedPubMedCentralGoogle Scholar
- 18.Agarwal V, Bell GW, Nam JW, Bartel DP (2015) Predicting effective microRNA target sites in mammalian mRNAs. eLife 4. https://doi.org/10.7554/eLife.05005
- 20.Bisognin A, Sales G, Coppe A, Bortoluzzi S, Romualdi C (2012) MAGIA(2): from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update). Nucleic Acids Res 40:W13–W21. https://doi.org/10.1093/nar/gks460CrossRefPubMedPubMedCentralGoogle Scholar