Global networks
You can download a whole predicted interactome for each of the 8 organisms as a single file. They are available as XML and TAB-delimited text files. The latter can be used with the program CytoScape, which can now import such files. See the format desription and details in README file in the same directory.
However, we strongly recommend using the visual interface of this web site.
Web interface of http://funcoup2.sbc.su.se
To start, you may just type in a gene symbol in the yellow box, select the respective organism, and click the button "Run". However, to use the full functionality of FunCoup web site, you may need to download and install JAVA Runtime Environment v.5 (version 1.5 by the old version numbering) or later from here -- and allow the browser using JAVA. The latter enables the functionality of jSquid applet -- with your consent, it will start automatically. The applet was specifically adjusted to the needs of the FunCoup web database and has multitudes of options to visualize gene sub-networks and manipulate them.

Then, while querying the database and reviewing the graphical output, you will soon realize that the number of available links for your query is usually too large. This is indicated with a message at the result web page: "Note that more links were found at this confidence. They were removed...". Essentially, neither the browser could visualize them, nor a human being would be able to grasp the displayed complexity. For this reason, a number of built-in procedures is trying to anticipate this overload and pre-filter the retrieved network -- hence the message. However, the procedures have a common feature: the filtering is confidence-driven and is not aware of your research focus. As a result, hundreds or even thousands of potentially important links are not shown. The following measures may help you re-focus the query around the gene(s) of your interest (let's call it X):