Try GeneMANIA. If you open up the advanced options, there's hundreds of networks to choose from. You can save the network from the file menu.
Then try STRING. This is the oldest and probably most widely used web tool for this purpose.
Other web-based network-construction tools for human include:
- FunCoup -- one of the few tools with regulatory interactions. Also has some nice display and clustering options
- FunctionalNet -- by one of the founders of the field of functional interaction networks.
It's worth trying all the tools because they use different network data sources and use a different algorithm to add nodes to your initial list to fill out the network.
The tools above combine network data from multiple sources (e.g. co-expression, protein interactions, sequence similarity, etc). There's a few other tools that focus only on one type of network data.
I found the following link by searching for "Online graphviz dot":
there's also: http://cytoscapeweb.cytoscape.org/
you can also create a 'fake' RDF file and use the W3C RDF validation service ( http://www.w3.org/RDF/Validator/ ) with the 'Graph' option
Respect to Cytoscape plugins, I would recommend Cytoprophet, that reconstructs networks based on protein and domain interaction databases. You just have to load a list of SwissProt homologs, and then the plugin does the rest.
I would definitely try the Reactome Functional Interaction (FI) Network plugin. It has been developed for analyzing cancer and other disease datasets.
Try looking into www.esyn.org
is a VERY easy network building , publishing and sharing tool - allows you to analyse your network - find what drugs interact with the proteins in your network and you can even import models from the biomodel database (https://www.ebi.ac.uk/biomodels-main/) and visualise them as Petri Nets
Hope it helps