Importing gene list and attribute values to string cytoscape

[slba...@uw.edu]

Hello,

I need basic help importing data into Cytoscape. I want to use string to build a PPI and I want to gradient color the nodes based on a specific value. The file I am using looks like this:

Entry,gene_symbol,MIIavg
Q14994,NR1I3,1
Q5XUX1,FBXW9,1
O00165,HAX1,1
Q9Y535,POLR3H,1
....

The tutorial from https://jensenlab.org/training/stringapp/ shows how to import a list of gene names. And I found other information on how to import a table. I need to combine this two functions.

Thanks,
SLB

[Alexander Pico]

Right. You can do both.  First, grab all the UniProt IDs, e.g., copied from the first column when opened in Excel. Then paste that into the STRING protein query tool at the top of the Network panel. This will generate a PPI from you list. Then, use Import Table from File... to import your full table, matching your uniprot column with the "query term" column in your STRING network. This will add your gene_symbol and MIIavg columns to the PPI network. Now you can do gradient color mapping etc.

 - Alex

[slba...@uw.edu]

Thanks so much for your reply! I followed your instructions and it imported the table headers (gene_symbol and MIIavg) but not the values. Any suggestions on why this may be?

Thanks, 

SLB

[Alex Pico]

You’ll want to double check the options you use during table import. I might have suggested the wrong ones, as I’m going by memory and not directly working with your files. The options need to specify the column in your STRING network and that matches the column in table your are importing, e.g., the columns that contain matching Uniprot IDs. That is the only way Cytoscape knows how to match up your data with the network.

If you can’t get it to work, then, you’ll need to provide the files. 

Hope this helps!

 - Alex

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[slba...@uw.edu]

Thanks so much this worked perfectly!

Not sure if I should start another thread or not but...

When I change the node size, it only does it for nodes without any edges. I currently have my nodes sized based on degree of connectivity but would like to make them all larger, keeping the proportions the same of course.

Thanks in advance,

SLB

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[piet molenaar]

Hi, 

You can set the default node size in order to increase the size of all nodes.

Click on the number in the Def. column of the Node size attribute

See image below

Hope this helps,

Piet

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Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Amsterdam University Medical Centers 
Meibergdreef 9
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[slba...@uw.edu]

Thanks for your reply. I attached images of the problem. The first image has size 30 (default?) and the second image I changed the size to 60. Notice only the non-connected nodes change in size. See also my size parameters in the image. 

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[piet molenaar]

Aha, in that case you should set the minimal value of the mapping size to 60 also. The mapping size overrides the default size.

Hope this helps

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Department of Oncogenomics, M1-131
Amsterdam University Medical Centers 
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

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

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