Dear Biostars, Hi

I have a list of **zebrafish** TFs (both family and members) upregulated in my condition1 and same data for condition2. (I also have a list of all transcription factores showing blastx hit with all my RNA-seq analysis)
I want to show them in a network (or maybe two networks).

I saw a [similar network][1] created using *Cytoscape*.

Could you please kindly help me in this issue? how to ready files as *cytoscape* input? how to create circular network showing each DE TFs in different colour?

or even another package/website for doing this ? 

Thanks

NOTE: e.g. of TFs families Up-regulated in my condition 1:

BX649453.2

baz2a

gtf2ird1

tcf3b

mef2d

lhx2b

PBRM1

cers5


  [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428447/figure/F6/
Hey Farbod,

You first need to decide whether to make a protein interaction network or co-expression network.

Then you can use [STRING][1], [GeneMANIA][2] or [BioGRID][3] to build your network.

Once the network is built, you can import it into Cytoscape and change the layout to circle it, and look the same as the picture you showed.


To change the color or shape of only a few nodes, you can add a new column to your network in cystoscape and for example enumerate only the node of interest, there you can only change the shape and color of that node without changing the other.

Best Regards,
Leite

  [1]: https://string-db.org/
  [2]: https://genemania.org/
  [3]: https://thebiogrid.org/