proteomics data with cytoscape

[Prashali Bansal]

hello all,

I am a newbie with cytoscape and have some basic questions to start with. I have proteomic data from 6 bait proteins (drosophila) and I want to construct an interaction network. So essentially what  I want is something like that all the proteins (which are being pulled down with the bait) be linked to their respective bait protein and then within this list, all the known interactions (including across bait networks) be also shown.
My strategy is to first import the entire drosophila proteome, then map my proteins on it, then filter . However, I am not able to find mapping option when I import my data. In earlier versions it seems to be present as "import -> table -> advanced -> show mapping options" where you could select what column to use for mapping. I am using version 3.5.1 and I cannot find the mapping option anymore. Is there any other way of doing it or perhaps a whole new strategy.

Thank you very much!!!

Prashali

[Scooter Morris]

Hi Prashali,
    You should be able to do what you want using "File->Import->Table->File", but I'm not convinced that's the best approach.  My suggestion would be to start by importing your proteomic data set and getting the network you generated.  Then, to enrich that network with data from public repositories, just select the protein names and paste them into the stringApp (File->Import->Network->Public repositories) [you'll need to load the string app first, of course].  Now you'll have two networks and you can merge them to see how many additional interactions you get.

-- scooter

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[Prashali Bansal]

thank you so much for the suggestion. Works well. Although I realised that String app does not well as well as exporting data from string.org. Anyways, this method worked nicely :)

On Friday, August 18, 2017 at 2:08:12 AM UTC+2, Scooter Morris wrote:

Hi Prashali,
    You should be able to do what you want using "File->Import->Table->File", but I'm not convinced that's the best approach.  My suggestion would be to start by importing your proteomic data set and getting the network you generated.  Then, to enrich that network with data from public repositories, just select the protein names and paste them into the stringApp (File->Import->Network->Public repositories) [you'll need to load the string app first, of course].  Now you'll have two networks and you can merge them to see how many additional interactions you get.

-- scooter
 
On 08/17/2017 02:23 PM, Prashali Bansal wrote:

hello all,

I am a newbie with cytoscape and have some basic questions to start with. I have proteomic data from 6 bait proteins (drosophila) and I want to construct an interaction network. So essentially what  I want is something like that all the proteins (which are being pulled down with the bait) be linked to their respective bait protein and then within this list, all the known interactions (including across bait networks) be also shown.
My strategy is to first import the entire drosophila proteome, then map my proteins on it, then filter . However, I am not able to find mapping option when I import my data. In earlier versions it seems to be present as "import -> table -> advanced -> show mapping options" where you could select what column to use for mapping. I am using version 3.5.1 and I cannot find the mapping option anymore. Is there any other way of doing it or perhaps a whole new strategy.

Thank you very much!!!

Prashali

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