Cytoscape is a software tool for the visualization of molecular interaction networks that has been adapted to work as a component of caWorkbench. This component is located in the Visual Area in the upper right of the application. It’s typically used to visualize gene regulatory networks reconstructed using the methodology described in "ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context", Califano et. al, (http://arxiv.org/abs/q-bio.MN/0410037). Aracne uses Mutual Information, an information theoretical measure, to compute the correlation between pairs of genes and infer a best-fit network of probable interactions. The resulting network of genes can then be visualized and modified in the Cytoscape panel. A full description of the capabilities and functionality of Cytoscape can be found at http://www.cytoscape.org/.
- Create network using the caWorkbench Reverse Engineering functionality. This functionality is described in the User Manual and the Reverse Engineering section of online help.
Note: The “Layout” menu item at the top of the Cytoscape panel reveals a large selection of options that can be used to re-orient the network-image. For example the network image below was generated by choosing the Layout> yFiles> organic.
1 Mouse select the section of interest on the graph or from the file menu Select> and the selection option desired. The selected nodes are highlighted yellow.
。 Multiple markers can be selected by holding down the Control key and clicking on the corresponding network nodes; or, by using the mouse to define on the graph a rectangular area containing several markers.
2 In the marker panel (in the Selection Area in the lower left), a Selected Genes panel is updated to reflect the number of genes selected.
The contents of the panel are dynamically updated as markers within the Cytoscape graph get selected/de-selected. A full description of the capabilities and functionality of Cytoscape can be found at http://www.cytoscape.org/.