[ensembl-dev] Pathway analysis

[Alessandro Vullo]

And I would also add Reactome as well:

http://www.reactome.org

which among other things maintain an Ensembl to pathway mapping file:

http://www.reactome.org/download/current/Ensembl2Reactome.txt

cheers

Alessandro


On 31/08/16 10:08, Matthew Laird wrote:
> Hi Matiss,
>
> In addition to Kieron's reply there are a number of other high quality
> sources of interaction and pathway data.
>
> InnateDB (http://innatedb.ca)
> IntAct (http://www.ebi.ac.uk/intact/site/index.jsf)
> Bind (http://bond.unleashedinformatics.com/Action?)
> Mint (http://mint.bio.uniroma2.it/mint)
>
> As well EBI maintains a registry of programatically accessible
> interaction data in PSICQUIC registry (
> www.ebi.ac.uk/Tools/webservices/psicquic/view), unfortunately this is
> still currently offline after a weekend data centre shutdown on campus.
> It should be back online soon.
>
> On 31/08/16 09:54, Kieron Taylor wrote:
>> Hi Matiss,
>>
>> You could try http://www.genome.jp/kegg/rest/keggapi.html
>>
>> We don't have a direct relationship with KEGG at the moment, so take the links with a little caution.
>>
>> Kieron
>>
>>
>> Kieron Taylor PhD.
>> Ensembl Developer
>>
>> EMBL, European Bioinformatics Institute
>>
>>
>>
>>
>>
>>
>>> On 3 Aug 2016, at 11:58, Matiss Ozols <matiss.ozols at manchester.ac.uk> wrote:
>>>
>>> Dear all,
>>> I am using many Ensembl tools, however I am wondering how I can retrieve an information about pathways each gene is involved in? I found KEGG pathways but not sure if they have API.
>>> I am using Python programming and would be great to have an API that retrieves this info for each of genes.
>>> I have about 500 genes that I need to know what pathways they are involved in.
>>>
>>> Hope you can help,
>>> Best regards,
>>> Matiss
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> --
> Matthew Laird - Ensembl Core Developer
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