![]() ![]() We can add the original published figure for this gene set as a Cytoscape annotation, to add context to the nodes. Set the Vertical spacing between nodes to 50 and Horizontal spacing between nodes to 80.Under Layout → Settings., select the Grid Layout. The gene set is already arranged with a grid layout, but we can make it a bit more compact.Set the default node fill color to light gray. ![]() In the Style interface, under Node Fill Color, create a continuous mapping for logFC, with the default ColorBrewer Red-Blue gradient.We can now add a simple visualization of the data on the set of nodes. Two new columns of data will be added to the Node Table. Select the ncbigene column as the Key column for Network, to match the Gene column of the data.Alternatively, drag and drop the data file directly onto the Node Table. Load the TCGA-Ovarian-MesenvsImmuno_data.csv file under File menu, select Import → Table from File.Download a local copy of TCGA-Ovarian-MesenvsImmuno_data.csv.The data is annotated with NCBI Gene identifiers, which is also what the nodes in the gene set are annotated with. Next, we will import experimental data from TCGA, comparing gene expression between two molecular subtypes of ovarian cancer (Mesenchymal and Immunoreactive). The gene set will appear as a grid of nodes in Cytoscape, similar to what it looks like at NDEx. To open the gene set into Cytoscape, click the Open in Cytoscape button in the lower right.Save the figure by right-clicking on it and selecting Save Image As.The page will display the gene set on the left and the published figure they were extracted from on the right. In the Network Name field, type in Possible interaction between PI3K/AKT/mTOR network and PIM in ovarian cancer to find the network by name.Navigate to Published Pathway Figure Analysis Set at NDEx. ![]()
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