extracting a subnetwork from a genelist

[OL]

Hi all!

I have a whole genome-scale Y2H network for my organism. I can import
it just fine in cytoscape, works great. I can create subnetwork from a
new sif file I make from my target genes. That is cumbersome and I can
likely miss interactions...
Thus, is there a way to load the whole genome network, query it with a
list of genes (let's say 50 that I found by mass-spec forming a
complex with my target gene) and extract that subnetwork with all the
interactions for those 50 proteins too?
Hope that makes sense. I've been looking in tutorials and in the
manual but I must be missing the right keywords...

Thanks

Olivier

[Maital Ashkenazi]

Hi Olivier,

Yes, that makes perfect sense.
You can do this using EnhancedSearch plugin. Install the plugin
through Cytoscape plugin menu. Then paste the list of genes into the
search box. Query genes will be highlighted. Then, do File--> New-->
Network -> From Selected Nodes, All Edges.

Hope this helps,
Maital

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[Olivier Lucas]

Dear Maital,

Thank you for writing and releasing ESP.  That is working just fine as you recommended.  Additionally, regarding ESP, I have been trying to use the degree:[1 to 3] attribute, which I interpret as recovering 1 to 3 levels of interactions, without success. Could you give me a query example for one gene to recover its interacting partners and the partners of the partners please.

Thanks,

Olivier

--
Olivier

[DARIO DI SILVESTRE]

Hi all!

I have a question!
from my network I wish ti select a sub-network of nodes.
Is there a plugin with allow me to select a path among more than 2 nodes?

thanks
dario

---

Date: Wed, 13 Apr 2011 05:53:13 -0400
Subject: Re: [cytoscape-helpdesk] extracting a subnetwork from a genelist
From: oluca...@gmail.com
To: cytoscape...@googlegroups.com

[giovanni scardoni]

Hi Dario,
I have developed a new version of the Pesca plug-in. We have introduce
this new feature:
Given a network and a list of nodes it computes the subnetwork
connecting all the nodes of your list. The nodes are connected through
their shortest-paths.
The final version have not been release, since we are developing other
features, but I can
give you a beta version. Tell me if you are interested on testing this plug-in.
thanks,
Giovanni

2011/4/13 DARIO DI SILVESTRE <d_di_si...@hotmail.com>:

--
Giovanni Scardoni
The Center for BioMedical Computing (CBMC)
University of Verona
Strada le Grazie, 15 -37134
Verona -Italy

[allan_k...@agilent.com]

Hi, Dario. I'd be interested in testing the new version of Pesca plugin.

Thanks,

AllanK

Allan Kuchinsky
Principal Project Scientist
Molecular Tools  
Agilent Laboratories

Agilent Technologies, Inc.
Santa Clara, CA, USA
408.553.2423
allan_k...@agilent.com

[giovanni scardoni]

Hi all,
the beta version of the Pesca3.0 plugin is available at
http://profs.sci.univr.it/~scardoni/centiscape/pescadownload.php

The plugin is stable, but there is only a short user guide. Before the next release I want to improve

the algorithm since it has problems if the network is too large. I think also that with some modifications it

can run faster.

Please let me know all your suggestions at:

giovanni...@gmail.com

Please, do not hesitate to contact me if you have any question about the plugin.

Thank you!

Giovanni

2011/4/20  <allan_k...@agilent.com>: