![]() ![]() (A) A cytoHubba analysis result using the example dataset galFiltered.cys in the Cytoscape. Two screen-shots showing centrality analysis with cytoHubba. An example of cytoHubba result using the Cytoscape example dataset galFiltered.cys is shown in Figure Figure1 1. Tutorials and demo video are available in the website ( ). Network topological features of nodes are retrievable in the data panel as options of node attributes. The sub-graph of essential nodes is extendable to include nodes that directly interact with these top-ranked nodes by the option of " check first stage node" in control panel | hubba. Next, top-ranked nodes of a particular scoring method are retrieved from the cytoHubba tab in Cytoscape control panel, listed in the result panel, and the sub-graph of these selected nodes are shown in the main window with a color scheme from highly essential (red) to essential (green). First, scores from all eleven methods are granted to each node in a preloaded PPI network by executing "compute hubba result" function in the cytoHubba options in cytoscape menu bar. The enhanced node retrieving function in cytoHubba control panel helps researchers to search and explore the network and to extract user interesting subnetwork.ĬytoHubba provides a simple interface to analyze a network with eleven scoring methods. To make the network analysis easier for biologists to utilize more network features, we compose cytoHubba plugin to execute our newly developed algorithms and several popular algorithms. Different methods focus on different topological features, or similar features with different scoring strategies. These plugins provide more centrality measures than other commonly used, but some other important features and recent developed methods are not included. For example, NetworkAnalyzer and CentiScaPe computes various topological network parameters for undirected and/ or directed networks. Several Cytoscape plugins can score and rank the nodes by network features. Via Cytoscape, the graphical view of a network is easy accessed, and multiple layers of information including large-scale, genome-wise experiments, and protein function annotations can be granted on the interactome. They found that the degree of a protein correlates with the essentiality of its gene in other word, proteins with higher degrees are more likely to be essential proteins.Ĭytoscape is an open platform with many plugins to expand both the visualization options and the network analysis power. applied this method on a protein-protein interaction network of baker's yeast ( Saccharomyces cerevisiae). For example, network centralities rank nodes of a biological network according to a given importance concept, and Jeong et al. Network analysis can help us understand the function of an individual node and the collaboration between other nodes. These data can be represented as networks, in which the nodes as surrogates for proteins, metabolites, or transcripts, are connected by edges to show the interactions, reactions, or regulations among nodes. Recent breakthroughs in high-throughput techniques lead experimental data deluges in genomics, proteomics, transcriptomics, metabolomics and interactomics. ![]()
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