clusterMaker: a multi-algorithm clustering plugin for Cytoscape

By J. H. Morris, Leonard Apeltsin, Aaron M. Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D. Bader, T. Ferrin. BMC Bioinformatics, 2011

613 citations recorded by the source corpus.

BackgroundIn the post-genomic era, the rapid increase in high-throughput data calls for computational tools capable of integrating data of diverse types and facilitating recognition of biologically meaningful patterns within them. For example, protein-protein interaction data sets have been clustered to identify stable complexes, but scientists lack easily accessible tools to facilitate combined analyses of multiple data sets from different types of experiments. Here we present clusterMaker, a Cytoscape plugin that implements several clustering algorithms and provides network, dendrogram, and heat map views of the results. The Cytoscape network is linked to all of the other views, so that a selection in one is immediately reflected in the others. clusterMaker is the first Cytoscape plugin to implement such a wide variety of clustering algorithms and visualizations, including the only implementations of hierarchical clustering, dendrogram plus heat map visualization (tree view), k-means, k-medoid, SCPS, AutoSOME, and native (Java) MCL.ResultsResults are presented in the form of three scenarios of use: analysis of protein expression data using a recently published mouse interactome and a mouse microarray data set of nearly one hundred diverse cell/tissue types; the identification of protein complexes in the yeast Saccharomyces cerevisiae; and the cluster analysis of the vicinal oxygen chelate (VOC) enzyme superfamily. For scenario one, we explore functionally enriched mouse interactomes specific to particular cellular phenotypes and apply fuzzy clustering. For scenario two, we explore the prefoldin complex in detail using both physical and genetic interaction clusters. For scenario three, we explore the possible annotation of a protein as a methylmalonyl-CoA epimerase within the VOC superfamily. Cytoscape session files for all three scenarios are provided in the Additional Files section.ConclusionsThe Cytoscape plugin clusterMaker provides a number of clustering algorithms and visualizations that can be used independently or in combination for analysis and visualization of biological data sets, and for confirming or generating hypotheses about biological function. Several of these visualizations and algorithms are only available to Cytoscape users through the clusterMaker plugin. clusterMaker is available via the Cytoscape plugin manager.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/71598cb1c487a2ddba64a570ff64028d1981d8ac

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

A travel guide to Cytoscape plugins (2012, background): “For this purpose, clusterMaker 32 offers access to many different network clustering algorithms in one convenient interface (Fig.”
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible (2016, background): “…for users to interact with, visualize and analyze STRING networks (49), including integrating additional data from public repositories or their own experiments, changing visual styles and applying algorithms for network layout, clustering (50), enrichment analysis (51,52) and network analysis (53).”
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma (2019, methodology): “Cytoscape: a software environment for integrated models of biomolecular interaction networks.”