PEPPER

Find meaningful pathways / complexes connecting a protein set members within a PPI-network using multi-objective optimization
### PEPPER PEPPER - Protein complex Expansion using Protein-Protein intERaction networks - **identifies meaningful pathways / complexes** as densely connected sub-networks from *seed* lists of proteins derived from pull-down assays (*i.e* AP-MS...). PEPPER resolves connection sub-graph discovery problems by using **multi-objective optimisation** involving two objective functions: (i) the **coverage**, a solution must contain as many proteins from the *seed* as possible, (ii) the **density**, a solution must contain as many interactions as possible. Since these objectives conflict, no single solution can be considered as dominating the others. To summarise the information from all solutions, PEPPER merges *Pareto solutions* into a final predicted protein complex by **maximising the modularity** using a greedy search. PEPPER further refines predictions by an integrated **structure- and function-based post-processing** pipeline to rank proteins that were added by the algorithm. This workflow orchestrates **external data integration** (GO annotations, known complexes matching) besides measuring **connectivity features** (topological coefficients). **References:** - C. Winterhalter, R. Nicolle, A. Louis, C. To, F. Radvanyi, and M. Elati. "PEPPER: Cytoscape app for Protein complex Expansion using Protein-Protein intERaction networks", *Bioinformatics*, August 2014. DOI: [http://bioinformatics.oxfordjournals.org/content/early/2014/09/01/bioinformatics.btu517 10.1093/bioinformatics/btu517] - M. Elati, C. To and R. Nicolle, Multi-objective optimization for relevant sub-graph extraction. In Learning and Intelligent OptimizatioN (LION'7), LNCS, Italy, 2013

1.5.1

Works with Cytoscape 3.0

Release Notes

Main changes: * Unhandled text format issue fixed * Link to publication added in About window

1.5.0

Works with Cytoscape 3.0

Release Notes

Main changes: * New input GUI to improve user-friendliness * Post-processing overall score computed as weighted arithmetic mean with tunable weights * Error-tracking pipeline improved * Cytoscape integrated help for Pepper

1.4.2

Works with Cytoscape 3.0

Release Notes

Main changes: * Unix OS compatibility issue fixed

1.4.1

Works with Cytoscape 3.0

Release Notes

Main changes: * NEWS, README, AUTHORS and LICENCE files added * source code folder added to .JAR file * user-friendliness improved with tooltips * expansion proteins color gradient improved

1.4.0

Works with Cytoscape 3.0

Release Notes

Main changes: - post-processing analysis based on: (i) topology, (i) known complexes and (iii) GO terms - genetic algorithm speed strongly improved - error handling - user-friendly interface

1.1.0

Works with Cytoscape 3.0

Release Notes

Main changes: - plugin visual output improved with specific node colours and shapes - results user interface modified to display solution miniatures when a result is selected - algorithm improvements

1.0.1

Works with Cytoscape 3.0

Release Notes

Algorithm execution time strongly reduced.

1.0.0

Works with Cytoscape 3.0

Release Notes

**Stable release** main features: - input user interface slightly changed to allow users choosing an existing network - custom network tables attribute to check whether a protein is in the set of interest - warning when low parameters affect algorithms execution time - small bug fixes

1.0.0.beta

Works with Cytoscape 3.0


CYTOSCAPE 3

Version 1.5.1

License Click here

Released 24 Sep 2014

Works with Cytoscape 3.0

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