Question: There any tools for gene regulation network visualizing?
gravatar for Kurban
2.5 years ago by
china/Urumqi/xinjiang academy of animal scinces
Kurban190 wrote:

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.

ADD COMMENTlink written 2.5 years ago by Kurban190

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.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by A3.9k

How dose TRRUST compare to STRING?

Cytoscape is definetly the way to go:


Other network analysis apps

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by YaGalbi1.5k

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.

ADD REPLYlink written 2.5 years ago by A3.9k
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