Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference.
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.


BACKGROUND
http://cytoprophet.cse.nd.edu.
Morcos
Faruck
F
Department of Computer Science and Engineering and Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. cytoprophet@cse.nd.edu
Lamanna
Charles
C
Sikora
Marcin
M
Izaguirre
Jesús
J
D000465:Algorithms; D016013:Likelihood Functions; D016941:Myxococcus xanthus / Q000235:genetics / Q000378:metabolism; D054730:Protein Interaction Domains and Motifs; D025941:Protein Interaction Mapping; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D012984:Software
D011506:Proteins