CyTRANSFINDER: a Cytoscape 3.3 plugin for three-component (TF, gene, miRNA) signal transduction pathway construction

BMC Bioinformatics

Software

Alessandro Savino¹  Gianfranco Politano¹  Alfredo Benso¹  Stefano Di Carlo¹  Monica Raimo²  Francesca Orso³  Daniela Taverna³ 

[1] Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Torino, Italy;Molecular Biotechnology Center (MBC), Via Nizza, 52, 10126, Torino, Italy;Dept. Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza, 52, 10126, Torino, Italy;Molecular Biotechnology Center (MBC), Via Nizza, 52, 10126, Torino, Italy;Dept. Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza, 52, 10126, Torino, Italy;Center for Complex Systems in Molecular Biology and Medicine, Via Accademia Albertina, 13, 10123, Torino, Italy;

关键词: microRNA;    Signal transduction pathways;    Data fusion;    Cytoscape;    Network analysis;    Pathway analysis;    Network modules;   

DOI  :  10.1186/s12859-016-0964-2

 received in 2015-11-25, accepted in 2016-02-19,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundBiological research increasingly relies on network models to study complex phenomena. Signal Transduction Pathways are molecular circuits that model how cells receive, process, and respond to information from the environment providing snapshots of the overall cell dynamics. Most of the attempts to reconstruct signal transduction pathways are limited to single regulator networks including only genes/proteins. However, networks involving a single type of regulator and neglecting transcriptional and post-transcriptional regulations mediated by transcription factors and microRNAs, respectively, may not fully reveal the complex regulatory mechanisms of a cell. We observed a lack of computational instruments supporting explorative analysis on this type of three-component signal transduction pathways.ResultsWe have developed CyTRANSFINDER, a new Cytoscape plugin able to infer three-component signal transduction pathways based on user defined regulatory patterns and including miRNAs, TFs and genes. Since CyTRANSFINDER has been designed to support exploratory analysis, it does not rely on expression data. To show the potential of the plugin we have applied it in a study of two miRNAs that are particularly relevant in human melanoma progression, miR-146a and miR-214.ConclusionsCyTRANSFINDER supports the reconstruction of small signal transduction pathways among groups of genes. Results obtained from its use in a real case study have been analyzed and validated through both literature data and preliminary wet-lab experiments, showing the potential of this tool when performing exploratory analysis.

【 授权许可】

CC BY   
© Politano et al. 2016