I am doing RNA seq whole transcriptome analysis. I have got 2100 up regulated genes. I have tried to create PPI network in STRING database but it not accept over 2000 nodes. Is there any way to create it?
To answer the question directly, download the data and visualize it using adequate software on your local machine, e.g. cytoscape or using R (see this tutorial).
However, with so many nodes, your network is just going to look like a big hairball whether you view it on the web or on your local computer. You should consider what it is you want to visualize. One approach could be to cluster proteins into "complexes" and visualize the network of "complexes" instead or maybe visualize subgraphs related to different aspects of the biology that interests you or apply some decomposition method to view the network data as e.g. a scatterplot.
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