ClueGO+Cluepedia

[massim...@gmail.com]

Hello everybody,
I have just started using ClueGO+Cluepedia and I have some difficulties in understanding what the toggle "Show all genes shared between pathways" does. Could anyone help me?
Thank you in advance,

Massimo

[Bernhard]

Hi Massimo,
"Show all genes shared between pathways" should do what it says (it should show as new nodes all genes shared between terms/pathways), but before you can use these toggle button options from CluePedia, please make sure that you increase to a maximum the number of genes visualized per term/pathway (this is switched off / set to 0 to speed up the network creation by default). If you set it e.g. to a max 1000 genes per term then you should be able to use all the visualization options of CluePedia (by default you only see the genes from you input list that mapped to term/pathways). I hope this answered the question.
Best

[Massimo Rizzi]

Hi Bernhard,
thanks for the prompt reply. I usually set CluePedia to show the maximum number of genes (i.e. set to 1000), so this toggle button is activated. As "shared genes" do you mean "bridge" genes, i.e., genes that are shared among those GO terms/pathways (since they actually belong to those GO terms) and that may not belong to the initial list of genes?
Thank you for your attention,

Massimo

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[Bernhard]

Hi Massimo, yes you are right, if you click on "show shared genes" you will see all bridge genes (they do not belong to the initial gene list, otherwise they would be shown already) common among GO terms/pathways. Genes from the initial list are always shown and have a red node label.
Best
Bernhard

On Friday, January 15, 2016 at 10:00:06 AM UTC+1, Massimo Rizzi wrote:

Hi Bernhard,
thanks for the prompt reply. I usually set CluePedia to show the maximum number of genes (i.e. set to 1000), so this toggle button is activated. As "shared genes" do you mean "bridge" genes, i.e., genes that are shared among those GO terms/pathways (since they actually belong to those GO terms) and that may not belong to the initial list of genes?
Thank you for your attention,

Massimo

Il 14/01/2016 21:12, Bernhard ha scritto:

Hi Massimo,
"Show all genes shared between pathways" should do what it says (it should show as new nodes all genes shared between terms/pathways), but before you can use these toggle button options from CluePedia, please make sure that you increase to a maximum the number of genes visualized per term/pathway (this is switched off / set to 0 to speed up the network creation by default). If you set it e.g. to a max 1000 genes per term then you should be able to use all the visualization options of CluePedia (by default you only see the genes from you input list that mapped to term/pathways). I hope this answered the question.
Best




On Thursday, January 14, 2016 at 3:18:21 PM UTC+1, massim...@gmail.com wrote:

Hello everybody,
I have just started using ClueGO+Cluepedia and I have some difficulties in understanding what the toggle "Show all genes shared between pathways" does. Could anyone help me?
Thank you in advance,

Massimo

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[Massimo Rizzi]

Thanks a lot!

All the best,

Massimo

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