PEANuTv3 Wiki Page

Installation Instructions

This tool has been compiled for Cytoscape verion 3.2 and up. If you want to install it, download the compiled jar file here and install it in Cytoscape via App Manager or via copying it to the '~/CytoscapeConfiguration/3/apps/installed/'. Creating a symbolic link from that directory to the jar file also works.

If you have problems downloading the required dependencies with PEANuT in Cytosacpe, run it either as administrator or download them as .zip file here. After downloading simply unzip the contents into you Cytoscape plugin folder. Note however that the zip file might contain slightly older file versions than what the databases provide.

Also please notify us when the downloader is not working! It happens from time to time that the databases we are using change their urls or formats. We can only fix it when we are aware of this problem! :)You can use this google group to get in direct contact with us.

For further documentation consult the documentation of the 2.x version found here:

https://sourceforge.net/projects/peanut-cyto/

Compilation Instructions

This App is an OSGi Bundle. Consult this page on how to set-up Eclipse and then import the code via git:

http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Create_a_Bundle_App_Using_IDE

Background

This App is a port of the PEANuT Plugin to Cytoscape 3.x. Extensions written against the Cytoscape 2.x API are called plugins. Cytoscape 3.x uses an API based on the modern OSGi model its extensions are called Apps. The purpose of the App is to carry out pathway enrichment analysis. We believe that there is a lack of tools for gene or protein network analysis presently (2013-2015). The pathway enrichment analysis tool PEANuT arose out of the need to develop such tools.

One of the main challenges in software development for biology is the integration of large-scale datesets. An example problem is the extraction meaningful information from a list of differentiall regulated genes. One ansatz to this problem is to the view the genes in the context of their psysical, genetic and regulatory interactions. For example, a cancer study might produce numerical values for the expression levels of a set of mutated genes, which are a part of bigger regulatory network. This set is termed a "focus" network. Focus networks can also be created based on a specific biological question such as the relation of two proteins of interest. Numerical values coming from functional genomics studies can be used to weigh the edges of the network.

PEANuTv3 (Pathway Enrichment ANalysis Tool for Cytoscape 3.x) is a Cytoscape 3.x App designed to annotate protein interaction networks with biological pathway information and to calculate their enrichment in focus networks with respect to a background network. The results can also be exported as a tab delimited file.

PEANuTv3 can be accessed under: https://sourceforge.net/projects/peanutv3/.

The original PEANuT 2.x plugin was implemented by Falko Hofmann in JavaTM, using both Eclipse Indigo for Java EE Developers (http://www.eclipse.org/) and Netbeans 7.1.2. (http://netbeans.org/).

PEANuTv3 was ported to the Cytoscape 3.x platform as an OSGi Bundle App using Eclipse and Maven by Viktor Senderov.

The user can choose between the three databases ConsensusPathDB (http://consensuspathdb.org/), Pathway Commons (http://www.pathwaycommons.org/) and Wikipathways (http://www.wikipathways.org/) to annotate her network. While ConsensusPathDB requires Entrez gene IDs as input, Pathway Commons and Wikipathways require UniProt accession numbers.
ConsensusPathDB and Pathway Commons are databases that contain pathway data collected from publicly available pathway databases (e.g. Reactome , KEGG; see the respective homepages for more information). WikiPathways is a database based on the “wiki principle” and provides an open platform dedicated to collaborative registering, reviewing and curation of biological pathways.

While Pathway Commons and WikiPathways work with a wide variety of organisms ConsensusPathDB is specialized on Human, Mouse and Yeast Pathways. When the user chooses to annotate her network of interest with ConsensusPathDB data, she can additionally import directed interactions from KEGG to increase the amount of vertex degrees.

Information from Pathway Commons is directly accessed over their web service API. Information from ConsensPathDB and WikiPathways is retrieved by downloading flatfiles from their webpages via the Apache Commons IO library (http://commons.apache.org/proper/commons-io/).

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Project Members:

• habermannlab (admin)