ReConn

Loads pathway data from the reactome server and integrates expression data.
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ReConn is a Java plugin that connects Cytoscape to the Reactome database. ReConn offers the user the following features: -Loading pathways by name. -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. -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. -ReConn can work also in the o-0posite 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. -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.
CYTOSCAPE 2

Version 1.0

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Works with Cytoscape 2.8

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