Multiscale community detection in Cytoscape.

Trey Ideker,Christopher Churas,Teresa M Przytycka,Fan Zheng,Song Cao,Santo Fortunato,Akshat Singhal,Dexter Pratt

doi:10.1371/journal.pcbi.1008239

Abstract

Detection of community structure has become a fundamental step in the analysis of biological networks with application to protein function annotation, disease gene prediction, and drug discovery. This recent impact creates a need to make these techniques and their accompanying visualization schemes available to a broad range of biologists. Here we present a service-oriented, end-to-end software framework, CDAPS (Community Detection APplication and Service), that integrates the identification, annotation, visualization, and interrogation of multiscale network communities, accessible within the popular Cytoscape network analysis platform. With novel design principles, CDAPS addresses unmet new challenges, such as identifying hierarchical community structures, comparison of outputs generated from diverse network resources, and easy deployment of new algorithms, to facilitate community-sourced science. We demonstrate that the CDAPS framework can be applied to high-throughput protein-protein interaction networks to gain novel insights, such as the identification of putative new members of known protein complexes.

Highlights

One of the fundamental features of a complex network is the notion of community, which can be defined as a group of nodes that are more densely connected with each other than they are to the rest of the network
As an important technique to probe the structural organization of a complex network, it has been successfully applied to many problem domains in systems biology, such as identifying protein complexes[1,2,3,4], cataloging ‘omics profiles[5,6,7,8], and prioritizing new disease genes [9,10,11]
Clustering, which relates to community detection at a single scale, is a well-established technique in network analysis and is supported by many applications such as Clustermaker2[12], CytoCluster[13], ClusterViz[14], and MCODE[15], which have been made available in bioinformatics environments like Cytoscape[16]

Summary

Introduction

One of the fundamental features of a complex network is the notion of community, which can be defined as a group of nodes that are more densely connected with each other than they are to the rest of the network. Detection makes it possible to build hierarchical representations of biological structure and function directly from networks[17,18,19]. These developments create a new challenge: to make multiscale community detection techniques and their accompanying visualization schemes available to a broad range of biologists. We present a software infrastructure to address these challenges, termed CDAPS (Community Detection APplication and Service), deployed as an App in the Cytoscape platform for network analysis. CDAPS invokes community detection and functional enrichment algorithms via REST (REpresentational State Transfer) queries to a remote service outside of the Java-based Cytoscape desktop environment (Fig 1). CDAPS provides an end-to-end pipeline that creates, annotates, visualizes, and interrogates hierarchical models based on multiscale patterns in networks

Design and implementation

Functional enrichment

Interaction sub-networks

Results