S I D E S
An Algorithm for Identifying Significantly Dense Subgraphs

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SiDeS (Significantly Dense Subgraphs) is a software that implements a recursive graph clustering heuristic, which is based on statistical significance of subgraph density.

Implementation of SiDeS is available in two different languages; in C and in Java as a Cytoscape plug-in.

SiDeS is primarily designed for the identification of groups of proteins that are likely to correspond to a modular process, such as a protein complex. Since such proteins are likely to interact densely with each other, they are expected to induce "unusually" dense subgraphs in the protein interaction network. In SiDeS, statistical significance is used as a measure to evaluate the interestingness of the density of a subgraph.

SiDeS can be used for any application that requires clustering of the nodes of a graph based on subgraph density.