cytoscape+DAVID?

[Aladeokin ADEREMI, CALEB]

Hi all,

(1) 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.

(2) 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. Many thanks.

-Aderemi.

[Scooter Morris]

Hi Aderemi,

1. Well, I didn't think DAVID output a PPI, but a list of enriched genes, right?  You can certainly import the enrichment values into Cytoscape (maybe by starting with your STRING network?).  You could also take a look at the enrichment map tutorial, which works with DAVID output.
2. Similar to above, you have a list of proteins, not a PPI.  To get a PPI network, I would start by using the stringApp, and then enter the list of identified proteins to get an initial network.  Then, you could use the identified phospho-proteins to highlight those that are phosphorylated (by adding a column?).

-- scooter