Filtering multiple nodes from network

[gtzotzos]

I'm a novice to Cytoscape and therefore a bit lost. 

The object of my exercise is the generate subnetworks from the M.musculus interactome (BioGrid or other). 

I have large lists of genes (> 1000) with specific phenotypic properties. I thought that I should be able to import a table (Excel file) in which the first column is the gene id and then use these ids to select the corresponding nodes in the interactome and generate a new network with these selected nodes only.

Using import from the File menu/Import table gives the following error message: Duplicate Column Name Found. I'm attaching a snapshot of the import window for easy reference.

I'd be grateful if anyone could provide some suggestions regarding (a) whether the above approach is sound, and if so (b) troubleshooting options.

Grateful in advance for any advice

George

[piet molenaar]

Hi George,
You can use Select → Nodes → From ID List File...

See documentation here: http://manual.cytoscape.org/en/stable/Finding_and_Filtering_Nodes_and_Edges.html#the-select-menu 

Hope this helps,

Cheers,

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
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