I performed a differential expression analysis and I have a list of DE human genes. now, I want to visualize DEGs by Cytoscape (showing up-regulated and down-regulated proteins with different shapes and set the size of the nods on the base of levels of expression.) but this work needs a network and expression data.how should I obtain these files? and after that what do I do with them?
Hi, just prepare the table with the names of the DE genes only and import via import from table in Cytoscape and just change its attribute to the Source. Now click OK, Cytoscape will give you warning no edge will be created, ignore it and just proceed. Now you have listed as nodes.
Now create another two-column file in which the first column contains DE genes name and another column contain an attribute, for example, you can give upregulated as 1 and down-regulated as 2. In addition if you have fold change data with you you can add 3rd column also. Now import from file menu but as a node attribute and select first node as your key. Once it's get imported you can now go to style and just go to node and change node shape discrete, and from select different shape for 1 & 2 which is up and down-regulated. You can use the same attribute column for changing color ( Red for up and green for down or whatever you like. Next for the node size, if you have fold change data then you can select continuously and give fold change data.
