GeneGO under Ontologies/Pathways in ClueGO/Cluepdia

[BIOMICS]

Dear all, 

Can anyone help if it is possible to include GeneGO under Ontologies/Pathways for creating networks in ClueGO/Clupedia. 

Also is there an alternative to GeneGO which can do the same outcome similar as GeneGO, the reason is when I do GeneGO against those available in ClueGO such as KEGG, Reactome and Wiki pathways most of the time I get less than 1% overlap between the GOs. 

Thanks in advance. 

Nara

[Alex Pico]

Forwarded to ClueGO app author listed here: http://apps.cytoscape.org/apps/cluego

[Bernhard]

Hi Nara, I never used GeneGO but if you have gene per pathway information you can create a file in the format you can see e.g. in the "/My_HOME_FOLDER/ClueGOConfiguration/v2.5.1/ClueGOSourceFiles/Organism_Homo Sapiens/Homo Sapiens_KEGG_Pathways_20.11.2017.txt.gz". Unzip this file and open it with e.g. Excel and you will see the format. Concerning the overlap of GeneGO and GO or KEGG I can not comment on because I never used it.
Best

[Narasimhan Kothandaraman]

thanks, Bernhard. 

---

From: Bernhard <gabriel...@gmail.com>
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Sent: Sunday, 25 February 2018, 22:41
Subject: [cytoscape-helpdesk] Re: GeneGO under Ontologies/Pathways in ClueGO/Cluepdia

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[Narasimhan Kothandaraman]

Hi Bernhard, 

Can I clarify in ClueGO analysis under KEGG Compounds is it possible to input lipids to create metabolite enrichment networks with genes. If it could be done what type of lipid ID should I use (e.g., KEGG_ID, SMILES_ID, InChiKey_ID or PubChem CID_ID). 

Thank you,

Nara

---

From: Bernhard <gabriel...@gmail.com>
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Sent: Sunday, 25 February 2018, 22:41
Subject: [cytoscape-helpdesk] Re: GeneGO under Ontologies/Pathways in ClueGO/Cluepdia

[Bernhard]

Hi Nara,
you can use for the moment only the KEGG compound IDs but you have to download the conversion (KEGG-Compound-ids...) file under downloads next to "Ontologies/Pathways". Then the ids like "C00001 Water" will be recognized by ClueGO when you map against KEGG compound ontology. You can mix them KEGG pathways and KEGG Compounds.
Best

On Sunday, February 25, 2018 at 4:00:08 PM UTC+1, BIOMICS wrote:

Hi Bernhard, 

Can I clarify in ClueGO analysis under KEGG Compounds is it possible to input lipids to create metabolite enrichment networks with genes. If it could be done what type of lipid ID should I use (e.g., KEGG_ID, SMILES_ID, InChiKey_ID or PubChem CID_ID). 

Thank you,

Nara

---

From: Bernhard <gabriel...@gmail.com>
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Sent: Sunday, 25 February 2018, 22:41
Subject: [cytoscape-helpdesk] Re: GeneGO under Ontologies/Pathways in ClueGO/Cluepdia

Hi Nara, I never used GeneGO but if you have gene per pathway information you can create a file in the format you can see e.g. in the "/My_HOME_FOLDER/ClueGOConfiguration/v2.5.1/ClueGOSourceFiles/Organism_Homo Sapiens/Homo Sapiens_KEGG_Pathways_20.11.2017.txt.gz". Unzip this file and open it with e.g. Excel and you will see the format. Concerning the overlap of GeneGO and GO or KEGG I can not comment on because I never used it.
Best


On Wednesday, February 14, 2018 at 9:51:36 AM UTC+1, BIOMICS wrote:

Dear all, 

Can anyone help if it is possible to include GeneGO under Ontologies/Pathways for creating networks in ClueGO/Clupedia. 

Also is there an alternative to GeneGO which can do the same outcome similar as GeneGO, the reason is when I do GeneGO against those available in ClueGO such as KEGG, Reactome and Wiki pathways most of the time I get less than 1% overlap between the GOs. 

Thanks in advance. 

Nara

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[Biomica]

Hi Bernhard,
I'm able to see only this file 'KEGGCompound.annotation_2016.06.27.txt.gz' under the ontologies download section. I could not find the file you mentioned 'conversion file- (KEGG-Compound-ids...)'. Please advice and also let me know where should I download the file for the installation.
Thank you,
Nara

On Friday, 2 March 2018 02:51:18 UTC+8, Bernhard wrote:
> Hi Nara,
> you can use for the moment only the KEGG compound IDs but you have to download the conversion (KEGG-Compound-ids...) file under downloads next to "Ontologies/Pathways". Then the ids like "C00001 Water" will be recognized by ClueGO when you map against KEGG compound ontology. You can mix them KEGG pathways and KEGG Compounds.
> Best
>
> On Sunday, February 25, 2018 at 4:00:08 PM UTC+1, BIOMICS wrote:
>
>
> Hi Bernhard, 
> Can I clarify in ClueGO analysis under KEGG Compounds is it possible to input lipids to create metabolite enrichment networks with genes. If it could be done what type of lipid ID should I use (e.g., KEGG_ID, SMILES_ID, InChiKey_ID or PubChem CID_ID). 
>
>
> Thank you,
> Nara
>
>
>
>
>
>
>
>

> From: Bernhard <gabriel...@gmail.com>
> To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
> Sent: Sunday, 25 February 2018, 22:41
> Subject: [cytoscape-helpdesk] Re: GeneGO under Ontologies/Pathways in ClueGO/Cluepdia
>
>
>
>
>
> Hi Nara, I never used GeneGO but if you have gene per pathway information you can create a file in the format you can see e.g. in the "/My_HOME_FOLDER/ClueGOConfiguration/v2.5.1/ClueGOSourceFiles/Organism_Homo Sapiens/Homo Sapiens_KEGG_Pathways_20.11.2017.txt.gz". Unzip this file and open it with e.g. Excel and you will see the format. Concerning the overlap of GeneGO and GO or KEGG I can not comment on because I never used it.
> Best
>
>
> On Wednesday, February 14, 2018 at 9:51:36 AM UTC+1, BIOMICS wrote:
> Dear all, 
> Can anyone help if it is possible to include GeneGO under Ontologies/Pathways for creating networks in ClueGO/Clupedia. 
> Also is there an alternative to GeneGO which can do the same outcome similar as GeneGO, the reason is when I do GeneGO against those available in ClueGO such as KEGG, Reactome and Wiki pathways most of the time I get less than 1% overlap between the GOs. 
> Thanks in advance. 
> Nara
>
>
>
>
> --
> You received this message because you are subscribed to a topic in the Google Groups "cytoscape-helpdesk" group.
> To unsubscribe from this topic, visit https://groups.google.com/d/topic/cytoscape-helpdesk/MvdKTxV90vI/unsubscribe.

> To unsubscribe from this group and all its topics, send an email to cytoscape-helpd...@googlegroups.com.

[Bernhard]

Hi Nara,
yes this is the file you should download (KEGGCompound.annotation_2016.06.27.txt.gz) then you should be able to enrich the selected KEGG compounds ontology with IDs like C00001. Try it out.
Best

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