Hi Biostars,
Please, kindly assist me in resolving the following problems urgently: (1) I conducted a proteomic analysis using the shot-gun approach, I have a list of identified peptides as well as a list of identified proteins and also a list of identified phospho-peptides as well as a list of identified phospho-proteins. Please, which of these lists is appropriate for uploading into cytoscape to build a (i) PPI network and (ii) a signaling network.
(2) I have been generating my PPI network with STRING and import into cytoscape for visualization and further analysis. However, I will like to import the text file of the PPI network which I downloaded from DAVID into cytoscape. Please, does any one know how to do this? Thanks.
Many thanks.
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written
by
O'kin-1 •
1 answer
Regarding question 1: What is appropriate depends on what you want to do. You can load anything into Cytoscape as long as it can be put in a format that the software can parse. Concerning question 2: the solution is to put your DAVID data into a format that Cytoscape can import. This is not complicated. Read the Cytoscape documentation and if needed, use your favorite scripting language to reformat the data.
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Any luck about my post? Thanks.
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