Question: Creating a network in Cytoscape with nodes that have the same name
gravatar for justp
3.4 years ago by
justp10 wrote:

I'm using Excel to compile genes involved in a pathway, that I'm getting from literature. I figured out that I can import an Excel file into Cytoscape to show interactions between different nodes. What I've essentially done is assign each node a separate number and this allows me to have interactions that shows nodes with the same name have different interactions. For example, I have a protein called NEDD4 (just a random example) that appears multiple times in my constructed pathway, but I want to show it as different nodes. I can do this by assigning a unique number to each node.

The problem is that I don't know how I can change the number to the actual name easily once I've uploaded the file into Cytoscape. I end up with just the number as the label for each node. If I use the actual name of the protein, then I think Cytoscape won't know which NEDD4 is which.

Is there some way I can easily change the names from the numbers? I have the protein name matching the corresponding ID number in my Excel file too.

cytoscape network pathway • 2.0k views
ADD COMMENTlink modified 3.4 years ago by solo777370 • written 3.4 years ago by justp10
gravatar for solo7773
3.4 years ago by
solo777370 wrote:

There is a solution

=========input data ===========

geneAid geneAproperty   geneB
1   NEDD4   a
2   NEDD4   b
3   NEDD4   c
4   NEDD4   d

===== import network ====

enter image description here

===== sort by name ====

enter image description here

==== change one node's name to NEDD4

enter image description here

=======watch out: select other nodes you want to rename and apply to all selected ========

enter image description here

====== bingo =====

enter image description here

If you find any good solutions, please share with me.

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by solo777370
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