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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

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    $\begingroup$ You don't build pathway maps from bioinformatics data, you build them from wet-lab experiments. $\endgroup$
    – Devon Ryan
    Jun 21, 2017 at 6:37
  • $\begingroup$ I agree with Devon about patways because pathways indicate there is a shared known function. Protein-protein interactions/regulations maps are however another thing where bioinformatics can help out. One of the better exampels is www.string-db.org. Other options are by looking for clusters of correlation/anti correlation in large volumes of expression data. $\endgroup$ Jun 21, 2017 at 7:00
  • $\begingroup$ @0x90 Could you please clarify your question? How do you define a pathway (The link is to the MAPK/ERK "pathway" in wikipedia)? This is linked with the Kristoffer's observation. And which representation do you want from a pathway (If you want any)? BTW you seem also interested in comparing representation of pathways if I understood correctly the last sentence, that would be a different question probably $\endgroup$
    – llrs
    Jun 21, 2017 at 9:16
  • $\begingroup$ What do you mean by bioinformatics data? $\endgroup$
    – llrs
    Jun 21, 2017 at 14:24
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    $\begingroup$ That's a very different thing to what your question is asking ("pathway map"). Please edit your question and clarify what you are trying to do. $\endgroup$
    – terdon
    Jun 21, 2017 at 16:13

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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/

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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. :)

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