I have multiple genes collected from diabetic patients, I need to find out the pathways related to these genes using KEGG, Reactome and Wikipathways.
I know how to do that but need to find out if the resulted pathways are related to Diabetes or not.
Please help me to do that, is there a tool or R package help me to find out diabetes pathways ?
The [rWikiPathways package in bioconductor][1] lets you search the database in a few different ways. Like the comments above, exactly how *you* define a "diabetes pathway" is up to you. For example, you can search for any pathway that mentions "diabetes" anywhere in the title or description and then filter for the human set:

    library(rWikiPathways)
    db.pathways <- findPathwaysByText('diabetes')  
    human.db.pathways <- db.pathways %>% 
        dplyr::filter(species == "Homo sapiens")
    human.db.pathways$name

There were 4 that popped up when I ran this snippet:

> [1] "Type II diabetes mellitus"

> [2] "Insulin signalling in human adipocytes (diabetic condition)"

> [3] "Polyol Pathway"

>[4] "16p11.2 distal deletion syndrome"

You can retrieve the WPID identifiers and other info from the same returned data frame.

Alternatively, you can seach by your favorite diabetes gene, e.g., INSR:

    findPathwaysByXref('INSR','H') # H denotes HGNC identifer for query xref

This returns 27 human pathways! The [bioconductor package][2] includes additional vignettes for other common use cases.


  [1]: https://bioconductor.org/packages/release/bioc/html/rWikiPathways.html
  [2]: https://bioconductor.org/packages/release/bioc/html/rWikiPathways.html