Question: Obtaining directionality of pathways
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gravatar for s.may-wilson
3 months ago by
s.may-wilson30
University of Edinburgh
s.may-wilson30 wrote:

I am attempting to use R to extract biological pathway information from several different online databases (specifically KEGG, Wikipathways and Reactome) and use that information in a larger project I am working on where I am attempting to gauge levels of pathway functionality.

An important aspect of my method is requiring the directionality of a pathway: I.e. knowing that GENE1 leads to GENE2 leads to GENE3 etc. This is actually also fairly useful for simpler things like plotting any pathways of interest.

As it stands, I have spent some time working with KEGG and have a working method for this using KEGGgraph which is generally used for plotting pathways, but I can use it to extract the directions of the edges between vertices.

What I need now is something equivalent for Reactome and Wikipathways. I haven't really looked at Wikipathways yet, but for Reactome specifically I'm not sure if I've hit a dead end or not. I can use the reactome.db package for extracting list of genes, but it doesn't give any information about direction.

So, what I need is some way of extracting the information from Reactome and Wikipathways specifically and knowing which gene connects to which gene and also (importantly) which direction this effect occurs in. Ideally this would be something that I could do in R, or at the very least a way of pointing to files I could download and read into R (automatically) that would contain this information.

Any help appreciated.

ADD COMMENTlink modified 3 months ago • written 3 months ago by s.may-wilson30

Not really an answer, just a pointer: https://bioconductor.org/packages/release/bioc/html/rWikiPathways.html

ADD REPLYlink written 3 months ago by Egon Willighagen5.3k

For WikiPathways, there is also a Cytoscape app[1] that lets you import pathways as directed networks. This can all be controlled from R via the RCy3 package[2].

  1. http://apps.cytoscape.org/apps/wikipathways
  2. https://bioconductor.org/packages/release/bioc/html/RCy3.html
ADD REPLYlink written 3 months ago by xanderpico350
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