how can I set the key for assigning gene names to a PPI in cytoscape
Lets assume I have a set of PPI as follows
O15145 P59998
O15145 O15511
P61158 P61160
P61158 P59998
P61158 O15511
I upload my network without any problem. Then I want to assign the proteins to their name. so I try to upload the gene names by table but it needs a key. If I use the following, it does not assign it to my network.
ProteinIDs Gene Name
O15145 ARPC3
P59998 ARPC4
O15511 ARPC5
P61158 ACTR3
P61160 ACTR2
What would you suggest?
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I am not sure what is going wrong for you. I saved your set of PPIs and your list of IDs/names as two tab-delimited files, loaded them into Cytoscape and just specified
shared nameasKey Column for NetworkandProtein IDsas key column in the preview table. I suspect there maybe some minor problem with the files you try to import, possibly you have some mix of tabs and spaces that makes Cytoscape not read the second file correctly.@Lars Juhl Jensen When I do that it becomes like this
Here are the properties for the Import columns from Table
Where to import Table Data -----> To NETWORK COLLECTION Network Collecton ----> Network.txt Import Data as : Node Table Columns
Key Column for Network : Shared Name (the protein ID I used) Case sensitive is ticked too
I imported both data as tab delimited files.
It looks correct to me. The fact that two of the names got mapped also suggests that it is right, but that some identifiers fail to match. Please double check both of your files to make sure that you do not, for example, have any space characters that have sneaked in before or after the content in the tab-delimited columns. What you do is right and works for me, so I can only assume that something is wrong with your files.