Interpretation of the gene scores in GeneMania

[Tang, Jing]

Dear Prof. Gary Bader,

We are currently trying GeneMania and a bit unclear about the interpretation of the gene scores. In the 2010 paper, it says that ‘we use label propagation to score all non-query genes’, however, I could find where it is mentioned about the query genes. I suppose the scoring of query genes is the same method that is used for non-query genes, i.e. based on the proximity of each gene to the other genes in the query list?

Thanks for the help.

Best,

Jing

 

 

 

 

Jing Tang, PhD, Group leader, Academy of Finland Research Fellow

Docent in Biometry

Network pharmacology fore precision medicine group

Institute for Molecular Medicine Finland, Helsinki Institute of Life Science,

University of Helsinki, Finland

https://twitter.com/netpharmed

https://www.fimm.fi/en/research/groups/tang

https://www.helsinki.fi/en/network-pharmacology-for-precision-medicine

 

 

[Tang, Jing]

Hi,

One more question: when using the Cytoscape plugin, it shows the ’Gravity panel’ that includes genetic variant legends. But in my application it is not relevant so is there a way to just remove this ‘Gravity legend’ panel?

Best,

Jing

[Christian Lopes]

Hi Jing,

I don't understand what you mean by Gravity Legend Panel from the GeneMANIA app.

Could you please send a screen shot of that panel?

Thanks,

Christian 

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[jing.t...@gmail.com]

Hi Christian,

It is the panel next to the 'Network Table'. Please take a look at the snapshot. Thanks.

[Christian Lopes]

Hi Jing,

I see... That panel is not created by GeneMANIA.

It seems it's from the Gravity app (http://gravity.pasteur.fr/results.html#network) and it does not look like you can remove it, unless you uninstall the app, of course.

Thanks,

Christian

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