need help with Bingo-GO analysis-URGENT

[snowhite snow]

Hi,

I am a beginner in Cytoscape. I am using latest version of Cytoscape i.e version 3.0.2

I have imported a network and now using Bingo app to do GO analysis for the network. When i m running Bingo, i am getting a new network with GO terms associated with the nodes.

I want to further categorize this network being generated by Bingo to functional subnetworks or modules. For example, I just want to have subnetwork with a particular GO term, say immune system development. How can i seperate my subnetwork with a particular GO term from rest of the chunk in the network having GO term which i am not interested in..

 

I hope i have made myself clear.

Hoping for an early response. I really need to solve this problem as soon as possible. Kindly help me

Thanks,

Snowhite

[Alexander Pico]

Hi Snowhite,

Once you select the nodes you want to separate, you can create a new subnetwork via File>New>Network>From selected nodes, all edges (or cmd-N on Mac)

 - Alex

--
You received this message because you are subscribed to the Google Groups "cytoscape-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-disc...@googlegroups.com.
To post to this group, send email to cytoscap...@googlegroups.com.
Visit this group at http://groups.google.com/group/cytoscape-discuss.
For more options, visit https://groups.google.com/groups/opt_out.

[snowhite snow]

Thanks Alex for replying. I did d way u mentioned in your reply. After that i have two queries:

1) When i am creating subnetwork then the nodes are showing GO ID as their labels. But i want to know what all proteins from my original network are their in a particular GO process, and finally want to show that subnetwork consisting of proteins, from my original network, associated with GO processes of my interest, as nodes.

2) In bingo output window i am selecting few GO processs by checking the boxes on their left, then clicking on select nodes (down right in the bingo window output). But none of the nodes are getting selected in my network. My aim here is to select simultaneously all related GO processes in the network so that i can create a subnetwork as mentioned in my first query in this post.

Thanks,

Snowhite

[Alexander Pico]

Thanks for the additional details. In order to accomplish #1 you would normally use the "select nodes" feature in the BiNGO output, just like you attempted to do in #2. And, indeed, this feature appears broken!  I had to run Cytoscape from the command line to display these hidden errors, and there is in fact a Java NullPointerException being called when that button is clicked (that's why you see nothing happen). I'll file a bug report and cc you on it.

In the meantime, there is a workaround. It's a lot of steps, but only takes minutes:

1. Find the GO terms you want in the BiNGO output table

2. Select all the corresponding "gene" fields (you can use shift or cmd for multi-select)

3. Copy into clipboard using keys (e.g., cmd- or ctrl-C)

4. Paste gene names into new text document (e.g., text edit or wordpad)

5. Add carriage returns after each ID, so that there is only one ID per line 

6. Save as go_genes.txt

7. In Cytoscapes menu: Select>Nodes>From ID List File…, choose your go_genes.txt

Voila! 

 - Alex

[Tim Hull]

Hi,

I just tested the "select nodes" feature, and it seems that it works here as expected. Are you using the "Get Cluster from Network" or the "Paste Genes from Text" option in BiNGO? I do see the exception you reported if you use "Paste Genes from Text", though in that case there is no source network - and as such it is not supposed to select anything. 

If you are indeed using the "Get Cluster from Network" option, do you have any sample data you can share that causes the exception?

Tim

[snowhite snow]

Hi Alex,

In step 5 when you mentioned "ID", did u mean GO ID or gene ID?

Do i have to paste gene names along with GO-term?

Can you please help me with carriage return and guide me with how to add it? I tried ^p and \n also but its not working.

Snowhite 

[Tim Hull]

Do you have some kind of example file you can provide which demonstrates the problem? Otherwise, I can't reproduce it here - when there is a network, the Select Nodes button seems to work as expected...

Tim

On Tue, Nov 26, 2013 at 2:41 AM, snowhite snow <snowhit...@gmail.com> wrote:

Hi Tim, 

I am using the "get cluster from network" option. and the network was imported using tab limited file from STRING database.

Snowhite