Linksets for miRTarBase 8.0 mmu and TargetScan for mmu

[JS1223]

Does anyone know how can i have the linkset for the miRTarbase v. 8.0 Mus musculus? Or is CyTargetLinker planning to launch it soon in their page? (https://cytargetlinker.github.io/pages/linksets/mirtarbase)

Moreover, is CyTargetLinker planning to launch the linkset for TargetScan Mus musculus?

Thank you all for the attention.

Yours sincerely.

[mkutmon]

Thank you for your message. I will try to create the two requested linksets as soon as possible.

[mkutmon]

@JS1223: I cannot find a release 8 for miRTarBase. Last release was version 7: http://mirtarbase.mbc.nctu.edu.tw/php/download.php.

That one is available on the linkset download page of CyTargetLinker: https://cytargetlinker.github.io/pages/linksets/mirtarbase.

[JS1223]

Dear @mkutmon

Thank you so much for your answers and attention.
The miRTarbase 8.0 can be found here:

http://mirtarbase.cuhk.edu.cn/php/index.php

https://academic.oup.com/nar/article/48/D1/D148/5606625

Thank you so much once again ☺️

[mkutmon]

Ah, thanks! Somehow I missed that one. I was always checking the old website apparently :(. I will create the new linksets and upload them as soon as possible.

[mkutmon]

@JS1223 I uploaded links to the mouse TargetScan linkset and also created the version 8 for miRTarBase. I am a little confused by that one because it contains the exact same numbers as version 7... I checked the downloaded files and they have the same number of rows, so I guess that is correct?

[JS1223]

@mkutmon Thank you so much for your availability and kindness providing the new linksets.

However, when i try to download the linksets this message appear: {"message": "Insufficient permissions", "code": "InsufficientPermissions"}

In relation to miRTarBase i also checked and in fact it has the same numbers as version 7. I will try to clarify this situation.

[mkutmon]

strange! it should work now. sorry about the delay.

[JS1223]

Dear @mkutmon

I still have one more question. I am trying to construct a network for 5 microRNAs using both linkesets miRTarbase 8.0 and TargetScan 7.2 for Mus musculus.

However, when i select an overlap threshold = 2 all the edges and targets for the 5 microRNAs disappear. Do you have any idea why is this happening?

[JS1223]

Here in attachment what is happening

[JS1223]

@mkutmon the proble is resolved! The overlap threshold (OT) function is only working in cytoscape version 3.7.2. and i was using version 3.8.0.

However, i cannot export the microRNA targets only present in the network with an OT=2 to ClueGO. Do you know how can i do it?