<p>Does anybody know how to plot a network similar to the one in the below TCGA paper?</p>

<p>http://www.nature.com/nature/journal/v517/n7536/fig_tab/nature14129_F5.html</p>

<p>More specifically, is there a tool to produce such visualization or was it created manually?</p>

Maybe you could make it with [OmniGraffle][1]. It has some nice network drawing tools. One thing that OmniGraffle offers that I don't think Illustrator offers is automatic management of connections between elements. For instance, you drag a node in the network and any connected edges are also redrawn. You can align nodes horizontally and vertically, to make a clean layout.

You might also investigate [the SBGN format][2]. One example in the relevant Nature paper shows [stimulation and inhibition][3], for instance. It looks like an [XML-based document format][4] that might lend well to automation, if you are making lots of these figures.

 [1]: https://www.omnigroup.com/omnigraffle
 [2]: http://www.sbgn.org/Main_Page
 [3]: http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.002.html?WT.ec_id=NPROT-201203
 [4]: http://www.sbgn.org/LibSBGN/Exchange_Format