CyTransfinder

CyTRANSFINDER is a new Cytoscape 3.x plugin that supports the reconstruction of small signal transduction pathways among groups of genes. 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 transaction pathways are limited to single regulator networks including gene/protein. However, networks involving a single type of regulator and neglecting post-transcriptional regulation mediated by miRNAs interacting with different transcription factors may not fully reveal the complex regulatory mechanisms of a cell.

We have developed CyTRANSFINDER, to enable users to infer three-component signal transduction pathways with the presence of miRNAs, TFs and genes based on user defined regulatory patterns. CyTRANSFINDER has been designed to support exploratory analysis, it therefore does not rely on expression data.

Developers

Gianfranco Politano

Stefano_DiCarlo_1

Stefano Di Carlo

How to cite CyTransfinder

The Sysbio development team  has invested a lot of time and effort in creating CyTransfinder as it is today. Please give credit where credit is due and cite CyTransfinder when you use it for your research activities.

CyTransfinder can be cited through this papers:

Politano G, Orso F, Raimo M, et al. CyTRANSFINDER: a Cytoscape 3.3 plugin for three-component (TF, gene, miRNA) signal transduction pathway construction. BMC Bioinformatics. 2016;17:157. doi:10.1186/s12859-016-0964-2

BibTEX

@Article{Politano2016,
author="Politano, Gianfranco
and Orso, Francesca
and Raimo, Monica
and Benso, Alfredo
and Savino, Alessandro
and Taverna, Daniela
and Di Carlo, Stefano",
title="CyTRANSFINDER: a Cytoscape 3.3 plugin for three-component (TF, gene, miRNA) signal transduction pathway construction",
journal="BMC Bioinformatics",
year="2016",
volume="17",
number="1",
pages="1--17",
issn="1471-2105",
doi="10.1186/s12859-016-0964-2",
url="http://dx.doi.org/10.1186/s12859-016-0964-2"
}

Downloads

CyTransfinder source code from TestGroup SVN Repository

CyTransfinder can be installed from the Cytoscape App Store

Tutorial

This short video shows a tutorial on how to use CyTransfinder.

The input files used in the video can be downloaded here:

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