The second, SLiMSearch can find new instances of known or potential motifs within the same network. SLiMFinder has previously been demonstrated as a suitable tool for mining the human interactome for SLiM mediated interactions. The first, SLiMFinder, is capable of finding novel motifs by analyzing a protein interaction network. SLiMscape consists of two primary analysis tools. Cytoprophet, another Cytoscape plugin, predicts domain and protein interaction networks however SLiMScape is the first to focus on SLiMs. Both novel and known motifs can be detected, providing a powerful tool for exploration and analysis of SLiMs within a protein interaction network. We have developed SLiMScape, a plugin which uses two of these tools to add SLiM discovery and search functionality to Cytoscape. Several predictive tools using many different methods have been developed to identify SLiMs. These often occur in intrinsically disordered regions and are involved in a number of functions such as binding, cleavage, subcellular targeting and post translational modifications. Many of these interactions occur between large globular domains but an estimated 15 - 40% are mediated by functional microdomains, of 3 - 10 amino acids in size called Short Linear Motifs (SLiMs). However, most of these experiments do not indicate the mechanism of interaction. High throughput experiments have greatly increased the number of known protein-protein interactions in the human interactome. This significantly aids in the discovery of novel short linear motifs and in visualizing the distribution of known motifs. SLiMScape provides a platform for performing short linear motif analyses of protein interaction networks by integrating motif discovery and search tools in a network visualization environment. To facilitate this SLiMScape automatically retrieves domains for each protein. The distribution of discovered or user-defined motifs may be selectively displayed and the distribution of protein domains may be viewed simultaneously. Data is presented using Cytoscape’s visualization features thus providing an intuitive interface for interpreting results. We present SLiMScape, a Cytoscape plugin, which enables both de novo motif discovery and searches for instances of known motifs. Cytoscape provides a visual interface for protein networks but there is no streamlined way to rapidly visualize motifs in a network of proteins, or to integrate computational discovery with such visualizations. GeneMANIA is actively developed at the University of Toronto, in the Donnelly Centre for Cellular and Biomolecular Research, in the labs of Gary BaderĪnd Quaid Morris, with input from an independent scientific advisory board.Computational protein short linear motif discovery can use protein interaction information to search for motifs among proteins which share a common interactor.
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