ClueGO Arabidopsis IDs

[Robert moseley]

Hi,

I'd like to change the Label source for Arabidopsis to output gene ID and not symbol id when using ClueGO? I found the below question and tried to do the same for Arabidopsis but I am having no success. What exactly do I need to change?

https://groups.google.com/forum/#!topic/cytoscape-helpdesk/Yi8D2hMDr9U

Thanks,

Rob M.

[Bernhard]

Hi Rob, normally it should work like described below on the helpdesk. Make sure you that you only have either the unzipped or the gzipped file of the Arabidopsis Thaliana.gene2accession_.... file in your Arabidopsis folder and not both. If you want the ATH ids as label, just duplicate the first column with the gene ids and name it "SymbolID" and remove the the other SymbolID column then it should work. Let me know .
Best

[Robert moseley]

Is there supposed to be a column with just the IDs in the Arabidopsis thaliana.gene2accession_2017.11.03.txt file? Mine does not. I attached a screenshot of what my file looks like. Is there another file that contains this column with the rows matched up? 

rob

[Bernhard]

Hi Rob, so you want to see instead of rrn26 the ArthMr001? If so, you have to split the data in the SymbolID column by | and copy the name you want to display in a final SymbolID column and remove the others. In the SymbolID column if there are more than one id per cell separated by a | , only the first id (normally the official gene name) will be displayed as label. So make sure that if you have several id per cell that the one you want to display is first. I attached here a new file. If you use this one you should see the Arth and AT ids as gene label. I renamed the previous SymbolID column to SymbolID_Old.
Best