Input file format

[indrani]

Hello ,

I am a new user of cytoscope. Can anyone please help to find any
documentation
regarding input file specifications for building networks.
I have a list of Entrez gene symbols which I wanted to create network
on
and use other cytoscope plugins for further analysis on this network.

Is this possible with cytoscope or it needs gene expression data for
input for building network.

Thanks,
Indrani

[JD]

a network can be build basically importing any kind of text file in the format

node1 node2 <attributes>

File -> import -> Network from Table

otherwise specific format has to be provided, but if you already have a list of gene

(and gene interactions) that's the easiest way

2010/3/31 indrani <indran...@gmail.com>

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[Gang Chen]

Hi,

I think you can try to create network from web service. Click here: http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual/ImportingNetworksFromWebServices, see the example #2 for example about NCBI entrez gene ID.

Gang

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Gang Chen
Computer Science Ph.D Candidate[1] & Biomedical Visiting Scientist[2]
[1] Central South University, Changsha, China,Cell Phone:13574886823
[2] Univ. of Texas Medical Branch, Galveston, USA, Cell Phone:(409)354-3186
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[De Boever Patrick]

Hi,

 

Importing gene list scan be done by renaming txt files containing IDs to .sif and then File>Import>Import Network and selecting your sif file.

All IDs will be loaded on the canvas and are available for analysis.

 

Patrick

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