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The Core&Peel web interface provides users with a tool to find dense subgraphs in a PPI network. The web interface allows you to:

run the Core&Peel algorithm with several parameter settings on custom data or on example data;
download the outcome of the algorithm and the sample datasets.

You can upload an ASCII file containing the list of the edges of the graph or use one of the five data files provided as default:

Dataset	Specie	Reference	proteins	interactions
DIP	yeast	Xenarios et al. 2000	4,637	21,107
Biogrid	yeast	Stark et al. 2006	6,686	220,499
String	yeast	Franceschini et al. 2013	5,590	133,082
Biogrid	homo sapiens	Stark et al. 2006	18,170	137,775
String	homo sapiens	Franceschini et al. 2013	12,717	193,105

The parameters that can be set are:

Neighborhood radius (r=1, r=2), r=1 the default is recommended value.
Minimum density of the subgraphs sought. maximum's default is 100\%.
Subgraph minimum size (either as an absolute number >=3, or as a proportion to the average degree of the PPI network).
Filtering policy (from more aggressive (f=0) to looser (f=2).

The parameters chosen will influence the running time of the method.

Reference:

[1] Xenarios, I., Rice, D.W., Salwinski, L., et al. (2000) DIP: the database of interacting proteins Nucleic Acids Res, 28, 289–291.

[2] Stark, C., Breitkreutz, B.J., Reguly, T., et al. (2006) BioGRID: a general repository for interaction datasets, Nucleic Acids Res, 34, D535–539.

[3] Franceschini A, Szklarczyk D, Frankild S, et al. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration, Nucleic Acids Res, 41, D808–D815.

Please, send any comments, bug reports, opinions to: BioAlgo Group