I am interested in doing a meta analysis study based on already published literature especially using protein based data to test one of my hypothesis and bring out the signalling networks acting in that particular condition.
The data which I would like to use would be of high- throughput such as derived from 2DE, Mass Spec, Shot Gun proteomics, etc. and also of specific studies targeting single proteins and determining their interactions or mechanisms.
I would like to know as to how to go about it, what all parameters to keep in mind, what statistical criteria and tests one should follow (if any).
Please suggest me good paper as well which mention about such methodology.
Looking forward to your kind suggestions...
You can start by using STRING ( http://string-db.org/ ) which can give a first idea for possible networks (known and predicted protein-protein interactions). It is possible to use multiple names ( http://string-db.org/newstring_cgi/show_input_page.pl?UserId=_0U8FZRKsfhm&sessionId=d2KAiWdd54kA&input_page_type=multiple_identifiers ) by giving a normalised list of gene names. Try it !
Yeah... that would be great. But once I get these known interactions... is it possible to enrich these networks by some database or prediction?
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