ReConn


ReConn is a plugin for Cytoscape developed by the biomodeling and bioinformatics
group at Eindhoven University of Technology.

Reactome is a publically available database aimed to gather information about all reactions that take place in a cell. Among other parameters, this information includes in which cell compartment a reaction takes place. Reactome therefore also contains reactions that transport metabolites between compartments. Such information is often essential for the correct modelling of a cell. The Reactome website however does not offer an optimal use of the information in the database. Therefore we developed ReConn - an extension of Cytoscape, an open source graph visualization tool written in Java. ReConn is a Java plugin that connects Cytoscape to the Reactome database.
ReConn offers the user the following features:

  1. Loading pathways by name.
  2. Generating a new pathway by taking a given metaboliteas a starting point. Cytoscape can then display all reactions that are related to the reactions that consumes the given metabolite.
  3. After a pathway has been loaded into Cytoscape, one can load data (e.g. from micro-array experiments) on top of it. This data is then visualized by changing the node colours. For instance, with micro-array data the colour and its intensity corresponds to the level of expression of the gene associated with the reaction.
  4. ReConn can work also in the oposite direction: the user can see how the data is mapped onto the various pathways of Reactome. Therefore one can select the pathway of interest by looking at the data, instead of starting with a pathway.
  5. ReConn can generate a subgraph containing all paths from one reaction to another. This is possible because of the graph-like data structure of Reactome. For clarity, one can limit the subgraph to paths shorter than a certain cut-off length. It is also possible to exclude certain reactions from this subgraph.

Features 2 and 5 are not present in any other software tool.
ReConn has many potential applications. For instance, the subgraph containing all paths between two reactions can be used for in silico knockout experiments. The other features are applicable in any analysis that requires data to be put into its biological context.

The zip file that contains ReConn can be downloaded here.
ReConn is distributed under the GPLv2 license.
And a zip containing the source can be obtained here.
Reconn uses one other library that should also be put into the Cytoscape plugins
directory, which are included in the zip file.
The libraries are:
MySQL JAVA connector from http://www.mysql.org


How to use ReConn? (A short manual)

For more information or questions send an e-mail to W.P.A.Ligtenberg@tue.nl