text: user734: I have some difficulties to understand/interpret the pathway map and how a gene-gene interaction list or DNA sequencing can map into pathways.
  In addition what's the difference between MARK/ERK pathway and the output of KEGG
  
  user931: See a project like Plant reactome, where they infer the pathways of all sequenced plant genomes using orthology to well annotated species.
  http://plantreactome.gramene.org/
  
  user824: As you alluded to in your question, KEGG does provide a curated set of enzyme and metabolite information. This information can be parsed and used to create a network that you can analyze to look at how gene products could be working together. Additional steps could include mapping transcriptome data to the map.
  See this paper as an example of how this can be done.
  I hope this helps. :)
  
original_text: 734: <p>I have some difficulties to understand/interpret the <a href="https://en.wikipedia.org/wiki/MAPK/ERK_pathway" rel="nofollow noreferrer">pathway map</a> and how a gene-gene interaction list or DNA sequencing can map into pathways.</p>
  
  <p>In addition what's the difference between <a href="https://en.wikipedia.org/wiki/MAPK/ERK_pathway" rel="nofollow noreferrer">MARK/ERK pathway</a> and the output of <a href="http://www.kegg.jp/kegg-bin/show_pathway?hsa05200" rel="nofollow noreferrer">KEGG</a></p>
   931: <p>See a project like Plant reactome, where they infer the pathways of all sequenced plant genomes using orthology to well annotated species.
  <a href="http://plantreactome.gramene.org/" rel="nofollow noreferrer">http://plantreactome.gramene.org/</a></p>
   824: <p>As you alluded to in your question, KEGG does provide a curated set of enzyme and metabolite information. This information can be parsed and used to create a network that you can analyze to look at how gene products could be working together. Additional steps could include mapping transcriptome data to the map.</p>
  
  <p>See <a href="http://biorxiv.org/content/early/2016/12/07/092304" rel="nofollow noreferrer">this paper</a> as an example of how this can be done.</p>
  
  <p>I hope this helps. :)</p>
  