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I have a relatively simply gene regulatory network I would like to visualize, complete with the common arrow and bar symbols used to show, respectively, which genes enhance or repress with other genes. Is there a way to typeset a gene regulatory network using something like LaTeX or Graphviz?

For very simple networks, I guess something like Photoshop or Illustrator would probably be the quickest solution, but these programs become very tedious as the size of the network grows even a little bit. What do people typically use for this type of task?

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If you have simple 1:1 connections or can list your data in that manner, you can try Cytoscape (freely available). There are numerous plug-ins to customize what you have in mind in terms of visualization.

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  • $\begingroup$ +1 for Cytoscape. I found it useful for looking at gene interaction networks pulled down from the yeast genome database. $\endgroup$
    – yamad
    Commented Feb 29, 2012 at 23:17
  • $\begingroup$ Thanks. One advantage of Cytoscape is its flexibility, simply provide a bunch of A-B links. Those links can be classified - stimulating/inhibiting - but need not be. $\endgroup$
    – Larry_Parnell
    Commented Mar 1, 2012 at 2:11
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I haven't tried it, but this StackOverflow answer suggests that you can import a GraphViz network into OmniGraffle (for Mac), which makes it very easy to produce a pretty network (much easier than Photoshop/Illustrator).

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  • $\begingroup$ I've used the Omni suite before, it's quite well designed software =) $\endgroup$
    – Rory M
    Commented Mar 3, 2012 at 12:11

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