Re: [Cytoscape-discuss] Target interaction protein list

[Scooter Morris]

Hi,
Can you say more about your proteomics experiment? You say you are
looking to identify protein complexes, so I assume you are doing some
kind of affinity experiment, maybe TAP/MS? If so, your target and
source should come from your experiment -- think of them as your list of
affinities. If you are doing some other kind of proteomics experiment,
I'm a little confused about how you're trying to identify complexes?

-- scooter

On 11/08/2012 11:31 AM, hlee15 wrote:
> Hi
>
> I am a beginner for cytoscape.
>
> I got data from proteomics experiments and am trying to use cytoscape
> for identifying protein complex networks.
>
> My question is about importing network from excel file. I can upload
> source interaction protein list.
>
> In case of target interaction protein list, what kinds of protein
> lists are uploaded? How can I find them (from web?)?
>
> I don't know about target interaction list.
>
> Thank you in advance.
> --
> You received this message because you are subscribed to the Google
> Groups "cytoscape-discuss" group.
> To view this discussion on the web visit
> https://groups.google.com/d/msg/cytoscape-discuss/-/ocVi5dgYOSwJ.
> To post to this group, send email to cytoscap...@googlegroups.com.
> To unsubscribe from this group, send email to
> cytoscape-disc...@googlegroups.com.
> For more options, visit this group at
> http://groups.google.com/group/cytoscape-discuss?hl=en.

[Scooter Morris]

In Cytoscape, the source and target just refer to the start and end of the edge.  In a traditional TAP/MS experiment, you should wind up with a list of proteins that are bound together and (hopefully) a measure of the affinity of that binding.   So, if protein A and protein B are bound together, list A as source and B as target.  If B is bound to protein C, then B would also be a source and C the target.  Since this is undirected, it doesn't matter which order you list (so A could be source and B target or the other way around). 

-- scooter

On 11/09/2012 11:07 AM, hlee15 wrote:

Could explain more about source and target?

The proteins I got from MS is source or target?

Or they are the same?

Thank you.

On Thursday, November 8, 2012 11:31:18 AM UTC-8, hlee15 wrote:

Hi 

I am a beginner for cytoscape.

I got data from proteomics experiments and am trying to use cytoscape for identifying protein complex networks.

My question is about importing network from excel file. I can upload source interaction protein list. 

In case of target interaction protein list, what kinds of protein lists are uploaded? How can I find them (from web?)?

I don't know about target interaction list.

Thank you in advance.

--
You received this message because you are subscribed to the Google Groups "cytoscape-discuss" group.

To view this discussion on the web visit https://groups.google.com/d/msg/cytoscape-discuss/-/V31Xy4tDoYUJ.