There any tools for gene regulation network visualizing?
Hello guys, I have a set of transcription factors and their target genes (TF-TG connection), and their expression data from RNA-seq at a certain treatment and control conditions. Here, I want to visualize this network, including hub and connection edges. Could you recommend some tools to do that? If the tool can evaluate the TF activities would be grate. Thanks.
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In TRRUST database I found a list of TF-target provided with activation-inhibition modes. Once I have done so;Firstly I inferred a gene regulatory network from my transcriptome (better differentially expressed between control and treatment), then I merged genes in my transcriptome with TRRUST to see which genes in my RNA-seq is regulated by a TF and the activation/inhibition mode. Then I imported my network to Cytoscape and by NetworkAnalyzer I seek connectivity within my network (genes those are likely more important with higher degree or the other centrality measures). I hope this was somehow close to whatever you want to do.
How dose TRRUST compare to STRING?
Cytoscape is definetly the way to go:
OmicsAnalysisCollection
Other network analysis apps
I used TRRUST just for downloading TF-target file, I then used this file to find the TF regulating my genes in RNA-seq. Finally I visualized a network of my genes in Cytoscape.