Journal Article

Cytoprophet: a <i>Cytoscape</i> plug-in for protein and domain interaction networks inference

Faruck Morcos, Charles Lamanna, Marcin Sikora and Jesús Izaguirre

in Bioinformatics

Volume 24, issue 19, pages 2265-2266
Published in print October 2008 | ISSN: 1367-4803
Published online July 2008 | e-ISSN: 1460-2059 | DOI: https://dx.doi.org/10.1093/bioinformatics/btn380
Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference

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Summary: Cytoprophet is a software tool that allows prediction and visualization of protein and domain interaction networks. It is implemented as a plug-in of Cytoscape, an open source software framework for analysis and visualization of molecular networks. Cytoprophet implements three algorithms that predict new potential physical interactions using the domain composition of proteins and experimental assays. The algorithms for protein and domain interaction inference include maximum likelihood estimation (MLE) using expectation maximization (EM); the set cover approach maximum specificity set cover (MSSC) and the sum-product algorithm (SPA). After accepting an input set of proteins with Uniprot ID/Accession numbers and a selected prediction algorithm, Cytoprophet draws a network of potential interactions with probability scores and GO distances as edge attributes. A network of domain interactions between the domains of the initial protein list can also be generated. Cytoprophet was designed to take advantage of the visual capabilities of Cytoscape and be simple to use. An example of inference in a signaling network of myxobacterium Myxococcus xanthus is presented and available at Cytoprophet's website.

Availability: http://cytoprophet.cse.nd.edu

Contact: cytoprophet@cse.nd.edu

Supplementary information: Examples and supplementary data are accessible at http://cytoprophet.cse.nd.edu

Journal Article.  1071 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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