cytoscape assign colors to different clusters

Cytoscape assign colors to different clusters plus#

Here we aimed to identify SUMO-1 binders selectively enriched for class II binding. Identification of SUMO binding partners is further complicated due to the typically transient and low affinity interactions with the modifier. Many previous studies to identify SUMO binders using pull-down or microarray approaches did not strategize on the SUMO binding mode. Class II binding is conveyed by the E67 loop region on SUMO-1. While interactors for the class I interaction, which involves binding of a SUMO-interacting motif (SIM) to a hydrophobic groove in SUMO-1 and SUMO-2/3, are widely abundant, only a couple of examples have been reported for the other two types of interactions. The small ubiquitin-like modifier (SUMO) is involved in various cellular processes and mediates known non-covalent protein-protein interactions by three distinct binding surfaces, whose interactions are termed class I to class III. clusterMaker is available via the Cytoscape plugin manager. Several of these visualizations and algorithms are only available to Cytoscape users through the clusterMaker plugin. The 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. Cytoscape session files for all three scenarios are provided in the Additional Files section. For scenario three, we explore the possible annotation of a protein as a methylmalonyl-CoA epimerase within the VOC superfamily. For scenario two, we explore the prefoldin complex in detail using both physical and genetic interaction clusters. For scenario one, we explore functionally enriched mouse interactomes specific to particular cellular phenotypes and apply fuzzy clustering. Results 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.

Cytoscape assign colors to different clusters plus#

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. The Cytoscape network is linked to all of the other views, so that a selection in one is immediately reflected in the others. Here we present clusterMaker, a Cytoscape plugin that implements several clustering algorithms and provides network, dendrogram, and heat map views of the results. 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. In 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.