Question: Diseases related pathways
1
gravatar for mrashad
8 weeks ago by
mrashad50
mrashad50 wrote:

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 ?

ADD COMMENTlink modified 7 weeks ago by xanderpico350 • written 8 weeks ago by mrashad50
2
gravatar for rpolicastro
8 weeks ago by
rpolicastro3.9k
Bloomington, IN
rpolicastro3.9k wrote:

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.

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by rpolicastro3.9k
1

This is probably the best you can do with databases. But nothing is really going to beat either a) Learning enough about the biology of diabetes that you know if the pathways are involved or b) showing your list of pathways to someone who has an indepth knowledge of Diabetes biology.

ADD REPLYlink written 8 weeks ago by i.sudbery11k

What is the difference between KEGG diabetes here: https://www.gsea-msigdb.org/gsea/msigdb/cards/KEGG_TYPE_II_DIABETES_MELLITUS.html and KEGG diabetes here: https://www.kegg.jp/dbget-bin/www_bget?ds:H00409 ??????

In the first link: I couldn't get the pathways itself, just gene set can be obtained, while in the second link: I can get the pathways itself. So which link do you think I can use?

ADD REPLYlink written 7 weeks ago by mrashad50
2
gravatar for xanderpico
7 weeks ago by
xanderpico350
xanderpico350 wrote:

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:

[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 includes additional vignettes for other common use cases.

ADD COMMENTlink written 7 weeks ago by xanderpico350

Thanks a lot for this fruitful answer

ADD REPLYlink written 7 weeks ago by mrashad50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1680 users visited in the last hour
_