![]() ![]() Nodes without annotated localization sites are positioned according to the location of their first neighbors. Localization annotation does not need to be complete, as reasonable results can be achieved with coverage as low as 30%. Localization information can be gathered from a number of resources (Gardy et al., 2006), including databases such as HPRD (Mishra et al., 2006) or prediction methods such as PSORTb (Gardy et al., 2005) for bacteria or Proteome Analyst (Lu et al., 2004) for eukaryotes. Potential products or outcomes of the network can be placed at the bottom of the diagram and clustered according to molecular function or any other attribute of interest.Ĭerebral can be used on any network for which subcellular localization annotation exists. Subcellular localization annotation is used to position nodes in layers, resulting in a cross-sectional view of the cell. We have therefore created Cerebral (Cell Region-Based Rendering and Layout), a Cytoscape plugin that automatically arranges networks of up to several thousand nodes using subcellular localization information.Ĭerebral generates layouts in the style of traditional biological pathway/cellular overview diagrams. These diagrams can be difficult for a user to explore with currently available network display tools-the networks are often too large, on the order of thousands of nodes, and many tools do not provide biological context to the diagram. Network diagrams are used for visualizing and understanding these interactions, interpreting high-throughput experimental data, generating hypotheses and sharing results. Systems biology is characterized by a focus on interaction networks-the biomolecules involved in a particular biological system or process, as well as the relationships between these components. ![]()
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