I found (Y2H etc.) to see relationships in ontologies, pathways etc.?
I have carried out a yeast two hybrid screen and far western to generate a list of proteins which interact with my protein of interest. I have a total of around 20 proteins that have been confirmed now through IP and pull downs. I would now like to see if there is enrichment of a certain biological process, ontology, signaling pathway etc. and produce some sort of visual map, diagram. Does anyone know what program (online and free if possible) I can use to plug in all my protein-protein interactions with my central protein used as the bait to see what the relationships if any there are between all these interacting proteins?
I recommend you mentha. Have a look, it's easy to use, and contains protein-protein interactions from different sources. It has been published few months ago on Nature Methods.
http://www.nature.com/nmeth/journal/v10/n8/fig_tab/nmeth.2561_F1.html
I would say Cytoscape can be a good option for that. It is open source and many plug-ins have been developed, including ClueGO and BiNGO for gene ontology annotation:
http://www.cytoscape.org/
http://apps.cytoscape.org/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666812/
I recommend cytoscape for variety of output option via plugins, one of my favorite plug ins is WizMapper which allows you to customize the network visualizations.
STRING (http://string-db.org) is also a very powerful option, although it doesn't have much flexibility as Cytoscape, it still provides lots of helpful analyses. You might see differences in certain pathway components, depending in what you used as bait.
Mentha: the interactome browser (http://mentha.uniroma2.it) also was very helpful for my network analyses. It uses different styles for network visualizations but it's nice to have an alternative.
STRING and Mentha if you want to have a snapshot first, then for more detailed network analysis, start learning Cytoscape. It might have a steep learning curve, so heads up!
Good luck
Burak
I recommend Ingenuity software. I can use this software one month free.
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