Building network with David+Cytoscape

Question

[O'kin-1]

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.

[O'kin-1]

Any luck about my post? Thanks.

[Jean-Karim Heriche]

The questions on this forum are answered by volunteers in their free time. If you're unhappy with the speed at which your question is dealt with please ask your local bioinformatician(s) for help. Also do not create an answer for something that is not answer. This makes the question appear as answered so you're even less likely to attract a real answer. I'm moving this to a comment.

Answer 1

[Jean-Karim Heriche]

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.