Convert xlsx file to XGMML

[Tara Ní Néill]

Hi,

I'm very new to Cytoscape and having some issues importing data. I have downloaded the  table of predicted targets of a microRNA from TargetScan from here:

https://www.targetscan.org/cgi-bin/targetscan/vert_71/targetscan.cgi?species=Human&gid=&mir_sc=&mir_c=&mir_nc=&mir_vnc=&mirg=hsa-miR-149-5p

https://www.targetscan.org/cgi-bin/targetscan/vert_71/targetscan.cgi?species=Human&gid=&mir_c=miR-149-5p&mir_sc=&mir_nc=&mir_vnc=&sortType=cs&incl_nc=0&allTxs=&text=1

It can only be downloaded as a txt or xlsx file, though I understand to import and make use of the Cy TargetLinker app the format must be xgmml. I've tried looking at how to convert this and am really struggling. I am running the most up to date version of Cytoscape on Windows 10. 

If anyone had any help or advice it would be much appreciated!

Best wishes,

Tara 

[Scooter Morris]

Hi Tara,

You can import your network into Cytoscape directly from your .xlsx file.  No need to convert it XGMML  In fact, "Tutorial 1" on the CyTargetLinker web site starts with an .xlsx file.   Just follow that tutorial and substitute your Excel file.  The columns may be different, but the key thing is to make sure you get the microRNA column selected as the Source Node.

-- scooter

[Tara Ní Néill]

Hi Scooter,

Thanks for getting back to me. I've been able to input the initial miR as an .xlsx file and was following the Tutorial 1. The problem I'm having is extending the regulatory network in Step 3, and bringing in the table above of predicted targets, as the file isn't an XGMML it can't be added. I suppose I could do this manually for each one? But was hoping if I can import all the predicted targets in one that would be much easier.

Best wishes,

Tara

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Tara Ní Néill BSc MSc

PhD Researcher

Biomaterials & Tissue Engineering Research Group,

Trinity Centre for Biomedical Engineering,

Mechanical and Manufacturing Engineering,

Trinity College Dublin,

Dublin 2,

Ireland.

[Scooter Morris]

Hi Tara,

  In step 3, you are supposed to load data from downloaded link sets that they provide.  Are you trying to provide your own link set?  If so, you are correct, it looks like CyTargetLinker really wants XGMML files.  The easiest way to get those is to import your linkset into Cytoscape using the excel file, and then save the resulting network as an XGMML file.  Then you can add it to the linkset directory.

-- scooter