I have found human proteins similar to my viral proteins. Now I am using this virus-similar human proteins to identify the interaction between my viral protein and human proteins. But I'm getting around 100 proteins that are similar to my one viral protein. Besides each of these 100 virus-like human proteins interact with "n" no. of proteins. So, the problem for me is how to get the GO annotation of such data. In which format shall I put data of all my 10 viral proteins to go foGo enrichment and generate graph using Bonferroni analysis? Second I could not understand how to generate graphic for my interaction data using cytoscape or some other software?
Go enrichment can be done with the web tool DAVID http://david.abcc.ncifcrf.gov/ (it will provide Bonferroni, Benjamini and FDR indexes).
For graphs of PPI I am using the pathway palette web tool. It is still easy to handle and you can use bioGRID and HPRD for different kinds of interactions
Thank you Mr.Matteo for ur help. Actually Sir, i want to know the input format for my dat so as to get a graph showing molecular abnd biological annotations of my virus-like human proteins as well as targets on the bonferroni scale in form of negative log value
On DAVID program, every source of protein is allowed.
Even affimetrix and siomilar formats are allowed.
You can choose, as an example, to use uniprotID or NCBIID.
Let´s say that the program is allowing almost every entry.
Good luck :D
To input interaction data into cytoscape you need it in an excel spreadsheet. For a very basic interaction map you need three columns, a source interaction (your gene) an interaction type (we have this input as 1) and a target interaction (the gene your source interacts with). you can have the same genes multiple times for the source and obviously for the target. In cytoscape (I use V2.8.3) click on file, import, network from table. then select the excel file and choose the relevant columns for the three options and import the network. Once you have the network you can add attributes (also in import) which can be used to change the size, colour etc of the nodes, for example you can have different colours for different GO terms. We've found with Cytoscape it's a case of playing with the software. I would potentially use a smaller dataset and try a few things first to really get an idea of what it can do.
Good luck.
thanks Andrew ..that was a great help.. i got about source interaction and target interaction. but could u plz clarify about "interaction type". i mean wat shd i put in this column like whether the interaction is identified by y2H, Co-IP or other methods or shallI simply put 1 as you have mentioned...Thanks again
We've always put the interaction in as 1 and then added additional information (like how the interaction is identified) as attributes. I think one of the great things about cytoscape is there are a number of different ways to get to the same result.