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 Molecular Signatures Database from Broad/UCSD has diabetes specific terms. Just search for 'diabetes' here to see what is included. You'll notice in the results that it also aggregates terms from other databases such as KEGG, Reactome, and Wikipathway as well.
The rWikiPathways package in bioconductor 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:
 "Type II diabetes mellitus"
 "Insulin signalling in human adipocytes (diabetic condition)"
 "Polyol Pathway"
 "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 includes additional vignettes for other common use cases.