Question: Creating a network in Cytoscape with nodes that have the same name
gravatar for justp
23 months 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 • 1.2k views
ADD COMMENTlink modified 23 months ago by solo777370 • written 23 months ago by justp10
gravatar for solo7773
23 months 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 23 months ago • written 23 months ago by solo777370
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1634 users visited in the last hour