question about identifying which pathway is shared between two genes

[Neil, Keith]

 

Hi, I’m wondering if I’m missing how to identify the pathway name/id in the cytoscape plugin app, for pathways (humancyc, reactome) from the network created for a set of genes.

 

I can click on the edge and get the edge table summary, which gives me the source of the pathway shared between the two genes, and a name like:

 

(from humancyc)

H__sapiens__3_-713497|H__sapiens__3_-702054|Pathway

 

But I don’t see any unique id / description of the actual pathway…  And didn’t see anything in the help documentation around this…

I can get it by going to the humancyc web site and looking at the two genes individually, but would be nice to avoid this step!

 

Am I missing something? 

 

Best regards, Keith

 

 

Keith Neil, M.Sc. Mol Biol. Genetics, B.Sc. BioPhysics

Bioinformatics, Research Informatics

 

+ 33.(0)534.63 31-37

+ 33.(0)534.63 22-86 (Fax)

keith...@evotec.com

www.evotec.com

Evotec (France) SAS

Bât.15 – Bureau 2106

195, route d‘Espagne,

31036 Toulouse CEDEX (France)

 

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[Gary Bader]

Hi Keith - GeneMANIA uses the SIF version of pathways from Pathway Commons (http://www.pathwaycommons.org/pc2/formats) Unfortunately we have not had resources to develop that feature in GeneMANIA so far, so you would need to download the pathway information separately to link up the information. We have a good set of pathways collected at http://baderlab.org/GeneSets

Best,
Gary

> On Nov 5, 2018, at 5:32 AM, Neil, Keith <Keith...@evotec.com> wrote:
>
>
> Hi, I’m wondering if I’m missing how to identify the pathway name/id in the cytoscape plugin app, for pathways (humancyc, reactome) from the network created for a set of genes.
>
> I can click on the edge and get the edge table summary, which gives me the source of the pathway shared between the two genes, and a name like:
>
> (from humancyc)
> H__sapiens__3_-713497|H__sapiens__3_-702054|Pathway
>
> But I don’t see any unique id / description of the actual pathway… And didn’t see anything in the help documentation around this…
> I can get it by going to the humancyc web site and looking at the two genes individually, but would be nice to avoid this step!
>
> Am I missing something?
>
> Best regards, Keith
>
>

> <image001.png>

> Keith Neil, M.Sc. Mol Biol. Genetics, B.Sc. BioPhysics
> Bioinformatics, Research Informatics
>
> + 33.(0)534.63 31-37
> + 33.(0)534.63 22-86 (Fax)
> keith...@evotec.com
> www.evotec.com
> Evotec (France) SAS
> Bât.15 – Bureau 2106
> 195, route d‘Espagne,
> 31036 Toulouse CEDEX (France)
>
> STATEMENT OF CONFIDENTIALITY.
>
> This email and any attachments may contain confidential, proprietary, privileged and/or private information.
> If received in error, please notify us immediately by reply email and then delete this email and any attachments from your system. Thank you!
>
>
>

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