Finding gene lists in a large network

[abed...@ymail.com]

Hi all,

I have a large network (9659 nodes with 39218 edges) and three gene lists that I imported them to Cytoscape (as a three networks without edge). I know that the genes of my lists are present in the large network but as my network is very large when I search genes, I can not see them. It is important for me to understand how these genes interact with each other in the large network and to see the neighbors of them.

Is there any tools in Cytoscape that I can get this information.

Kind Regards,

Maryam

[piet molenaar]

Hi Maryam,

You can select nodes from an id list file in the large network (see documentation here http://manual.cytoscape.org/en/stable/Finding_and_Filtering_Nodes_and_Edges.html#the-select-menu). Another way is to add an additional annotation column to your id lists and use that as annotation to the large network (http://manual.cytoscape.org/en/stable/Node_and_Edge_Column_Data.html#import-data-table-files). This will enable selection on the annotation attributes you specified (http://manual.cytoscape.org/en/stable/Finding_and_Filtering_Nodes_and_Edges.html#filters)

Hope this helps,

Piet

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Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626

[Scooter Morris]

Hi Maryam,
    Two suggestions for you.  First, install setsApp -- that will be useful for you (see below).  Second, use the Select->Nodes->From ID List file... to actually select the nodes of interest.  Once they are selected, you can use the setsApp to "remember" the selection (click the "+" at the upper left of the App panel).  Once you have your three sets defined, if you double-click on them, they will be selected in your network.  Your ID list file needs to have the same IDs as the "name/shared name" field in your network.  This will allow you to *not* have to create your three separate networks.

Hope this helps!

-- scooter

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