Hi all,
First a general question:
Does anyone know of a good biological pathway database comparison? Is KEGG an extensive one, or are all those databases for a specific type of pathways?
And the more detailed one:
Basically what I want is, in an automated fashion, for a list of genes (ENSG###) -> get all pathways in which the transcripts/proteins of a gene play a role.
The closest I have come so far is by using the Ensembl perl api and KEGG perl API:
So far, so good, it works, but there aren't many genes in my lists with an annotated pathway (around 10%)...making me wonder whether KEGG is a good resource for listing all possible pathways annotated.
Does anyone know a better workflow for this?
Thanks,
Stef
First a general question:
Does anyone know of a good biological pathway database comparison? Is KEGG an extensive one, or are all those databases for a specific type of pathways?
And the more detailed one:
Basically what I want is, in an automated fashion, for a list of genes (ENSG###) -> get all pathways in which the transcripts/proteins of a gene play a role.
The closest I have come so far is by using the Ensembl perl api and KEGG perl API:
- Ensembl API: make gene object with Ensembl id ( ENSG#### )
- Ensembl API: get the unigene id ( using $gene->get_all_DBLinks )
- KEGG API: retrieve pathways ($serv->KeggGetPathwaysByGenes )
So far, so good, it works, but there aren't many genes in my lists with an annotated pathway (around 10%)...making me wonder whether KEGG is a good resource for listing all possible pathways annotated.
Does anyone know a better workflow for this?
Thanks,
Stef
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