Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. Join them; it only takes a minute:

Sign up
Here's how it works:
  1. Anybody can ask a question
  2. Anybody can answer
  3. The best answers are voted up and rise to the top

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?

share|improve this question
up vote 7 down vote accepted

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.

share|improve this answer
+1 for Cytoscape. I found it useful for looking at gene interaction networks pulled down from the yeast genome database. – yamad Feb 29 '12 at 23:17
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. – Larry_Parnell Mar 1 '12 at 2:11

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).

share|improve this answer
I've used the Omni suite before, it's quite well designed software =) – Rory M Mar 3 '12 at 12:11

Your Answer


By posting your answer, you agree to the privacy policy and terms of service.

Not the answer you're looking for? Browse other questions tagged or ask your own question.