Dear everybody,
I use gProfiler to identify the TF enrichment analysis and then extract the file *.gem to import to the Cytoscape for drawing the TF network map. But the result is quite messy because each TF has some binding motifs, each binding motif have links with many genes. How can I combine the binding motifs of the same TF into one category like the enclosed graph?
Have you tried to use STRING before using Cytoscape? You just need to put your predicted genes, and it will appear a lot of ways to combinate your data. After that, you can export your file and keep working on Cytoscape (in a more clear manner).
Maybe it would be helpful.
STRING: https://string-db.org/
Good luck!
I see, I did the same thing. You just needs to arrange your input files according to your desired network, like nods or edges. Further, I suggest you watch some videos on YouTube, it will really help you. It is very easy, you just needs to understand the Cytoscape and how you can manipulate it.
Hi Ho Nguyen Tuong ,
Cytoscape generates network as you asked. Its open source tool please refer (https://cytoscape.org/)
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