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I would like to download all the gene pathways and genes of each pathway. Preferably, gene length of each gene as well. It would be a lot more convenient if there is an R package.

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    $\begingroup$ in what format do you want the pathways? You can bulk download the SBML files. Also, please clarify what you mean by "download the genes of each pathway". $\endgroup$
    – WYSIWYG
    Apr 21 '14 at 9:22
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    $\begingroup$ What pathways? From which database? What species? $\endgroup$
    – terdon
    Apr 21 '14 at 10:58
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Try using KEGG REST.

http://rest.kegg.jp/link/pathway/hsa ## list of all genes and pathways in Humans

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  • $\begingroup$ Do you mind showing me how you got this file? $\endgroup$
    – user258682
    May 4 '14 at 17:03
  • $\begingroup$ You can find it in the rest page. $\endgroup$ May 9 '14 at 6:42
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If you're working with BioCyc pathways you can use their REST-API for batch-downloading all genes for their pathways. You can run a wide range of queries including BioVelo-queries for all genes/compounds in a specified pathway, all pathways in organism etc. A query for all the pathways in B. subtilis would look like:

http://biocyc.org/xmlquery?[x:x%3C-bsub^^pathways]

Where you get an XML with the Cyc-IDs for the pathways which can be used to search for the genes. A query for all genes in the Arginine synthesis pathway in B. subtilis would then look like:

http://biocyc.org/xmlquery?[x:y:=bsub~argsyn-pwy,x%3C-%28genes-of-pathway%20y%29]&detail=full

Which returns an XML with information regarding the genes, start and end positions including (i.e. gene length). Since I don't work very much in R I don't know if there exists an R-package. But it is very straightforward to write Python scripts for downloading and XML-parsing.

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