Importing Node and edge files generated by WGCNA to cytoscape

[purushoth]

Hi all

Can anyone tell me how to import Node and Edge file generated by WGCNA to the cytoscape to run Network analyzer and to view the scale free network. There is a import option in cytoscape but, when i import as a table anyone table(node or edge) only i am able to import. How to import both node and edge to view the network in cytoscape?

I am trying hard to complete this task,

your response is highly appreciated.

Purushothaman

[Alexander Pico]

See "Option B" in this Cytoscape tutorial. It walks through how to import networks from tables. And there is a link to a tutorial for Network Analyzer at the App Store:

http://apps.cytoscape.org/apps/networkanalyzer

If you still have trouble importing, please provide more details. What are your columns and rows? What specific steps are not making sense? etc.

 - Alex

[Dr. N. Purushothaman]

Hi Alex

Thanks for the response. Actually i am trying to view scale free network using network analyzer plugin at cytoscape using the node and edge files generated using WGCNA analysis. When i am trying to import the node and edge file to cytoscape, it is asking to mention the start node, target node and interaction type, i do not know what does it means. For your information i am attaching the node and edge input file and screen shot of cytoscape where i used to input my files.... Looking for your response...

Purushothaman

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[Alexander Pico]

Easy. Source Interaction = "fromNode" and Target Interaction = "toNode". For Interaction Type, you can leave it as default to choose "direction". You can also click on headers for "weight" and other columns to load them as Edge Attributes.

Here's a tutorial on network importing that might help explain the concepts in more detail:

http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Getting_Started_with_Cytoscape#Option_B:_Open_a_text_or_Excel_file

Or this chapter in the manual:

http://cytoscape.org/manual/Cytoscape2_8Manual.html#Import Free-Format Table Files

 - Alex

[Dr. N. Purushothaman]

Hi Alex

Thanks for the info. I tried in this way, but when i started analyze network, it is keep showing "analyzing network" message for long time but no progress at all. I have attached my input file, can you try this. 

Purushothaman

[Alexander Pico]

Everything appears to be working properly. It's just a very large network. I simply took a small subset of your 22MB file and was able to import and run Network Analyzer just fine.

The performance scales with the hardware (mostly RAM) that you are running with. So, on a laptop with even 4-8GB, this is too much. You'll need to pre-filter your network prior to running Network Analyzer or load Cytoscape on a cluster with a lot more RAM.

 - Alex

[hyeonji park]

Perhaps, I have 5 modules. each module is 100~1000 genes.

WGCNA exported 2 files. edge and node. 

So I import edge file to cytoscape. but how to node file? 

node file contained ensembl gene id, gene symbol, and module name. what source, what target, what direction??? 

and how to interaction edge, node file ? edge file have not module name, but have gene information. 

- hyeonji

2012년 10월 16일 화요일 오전 8시 27분 52초 UTC+9, Alexander Pico 님의 말:

Purushothaman

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