ReNE

ReNE plugin, is a new Cytoscape 3.x plugin, which enables integration, merging, enhancement, visualization, and exporting of pathways from multiple repositories. It enables to import pathways from the KEGG and Reactome online repositories or from any standard OWL/XML data format that the Cytoscape import procedure acceptscustom file formatted according to one of the file formats accepted by Cytoscape. ReNE also enables to enhance the imported networks with transcriptional, post-transcriptional and translational information. It therefore represents a very interesting tool to enable an easy integration of multiple biological information into a single network that can be then analyzed and explored using the large set of tools provided by the Cytoscape ecosystem.

Developers

Gianfranco Politano

How to cite ReNE

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

ReNE can be cited through this paper: 
Politano G, Benso A, Savino A, Di Carlo S (2014)
ReNE: A Cytoscape Plugin for Regulatory Network Enhancement. PLoS ONE 9(12): e115585. doi:10.1371/journal.pone.0115585

BibTEX

@article{politano2014rene, 
title={ReNE: A Cytoscape Plugin for Regulatory Network Enhancement}, 
author={Politano, Gianfranco and Benso, Alfredo and Savino, Alessandro and Di Carlo, Stefano}, 
journal={PloS one}, 
volume={9}, 
number={12}, 
pages={e115585}, 
year={2014}, 
publisher={Public Library of Science},
keywords = {Gene regulation, Gene targeting, Genetic networks, MicroRNAs, Network analysis, Parkinson disease, Transcription factors, User interfaces},
url = {http://www.plosone.org/article/related/info%3Adoi%2F10.1371%2Fjournal.pone.0115585},
doi = {10.1371/journal.pone.0115585}}

Downloads

Install ReNE from the Cytoscape App Store
Download ReNE source code from SysBio SVN Repository

2 thoughts on “ReNE

  • great app but seems need a bit of an update. Intronic miRNA search does not always work. And miRbase has been updated to Version 21 while the app is still using Version 18 names

    • Dear Chris,

      thanks for the comment. The issue with the intronic miRNA search should be now fixed. Regarding the miRbase version, we are working on the update. This unfortunately is taking some time since the API to access al Das are not readily available.

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