<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>

CC BY-SA 3.0
2017-06-21T19:34:57.207Z
2017-06-21T19:34:57.207Z
G_Hannigan
<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>

CC BY-SA 3.0
2017-06-21T09:21:15.913Z
2017-06-21T09:21:15.913Z
Dan
<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>

CC BY-SA 3.0
2017-06-21T06:37:28.497Z
You don't build pathway maps from bioinformatics data, you build them from wet-lab experiments.
Devon Ryan
CC BY-SA 3.0
2017-06-21T07:00:57.290Z
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.
Kristoffer Vitting-Seerup
CC BY-SA 3.0
2017-06-21T09:16:06.330Z
@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
llrs
CC BY-SA 3.0
2017-06-21T14:24:01.957Z
What do you mean by bioinformatics data?
llrs
CC BY-SA 3.0
2017-06-21T15:48:04.580Z
@Llopis I mean how do you find the affected pathways from a gene-gene or protein-protein interaction list?
0x90
CC BY-SA 3.0
2017-06-21T16:13:36.500Z
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.
terdon
CC BY-SA 3.0
2017-06-21T17:34:46.537Z
@terdon I am not sure, how to properly rewrite the question.
0x90
CC BY-SA 3.0
2017-06-21T17:37:55.927Z
I can't help, I'm afraid since I don't know what you are trying to do :) A good start would be to show us an example of the data you have and an example of the kind of output you would like from it. Your links to wikipedia seem strange. What are we supposed to take from that? Also, gene-gene interactions (gene regulatory networks) are not the same as protein-protein interactions (which are closer to what rection pathways are). So it is really hard to understand what you're asking.
terdon
<gene><ngs><phylogenetics><pathway><kegg>
How can I find the relevant pathway map from gene-gene or protein-protein interaction list?
# How can I find the relevant pathway map from gene-gene or protein-protein interaction list?

(Asked by: username_0 on 2017-06-21)

I have some difficulties to understand/interpret the [pathway map](https://en.wikipedia.org/wiki/MAPK/ERK_pathway) and how a gene-gene interaction list or DNA sequencing can map into pathways.

In addition what's the difference between [MARK/ERK pathway](https://en.wikipedia.org/wiki/MAPK/ERK_pathway) and the output of [KEGG](http://www.kegg.jp/kegg-bin/show_pathway?hsa05200)

**Tags:** gene, ngs, phylogenetics, pathway, kegg
> **Comments:**
> **username_1**: You don't build pathway maps from bioinformatics data, you build them from wet-lab experiments.  
> **username_2**: 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.  
> **username_3**: @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  
> **username_3**: What do you mean by bioinformatics data?  
> **username_0**: @Llopis I mean how do you find the affected pathways from a gene-gene or protein-protein interaction list?  
> **username_4**: 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.  
> **username_0**: @terdon I am not sure, how to properly rewrite the question.  
> **username_4**: I can't help, I'm afraid since I don't know what you are trying to do :) A good start would be to show us an example of the data you have and an example of the kind of output you would like from it. Your links to wikipedia seem strange. What are we supposed to take from that? Also, gene-gene interactions (gene regulatory networks) are not the same as protein-protein interactions (which are closer to what rection pathways are). So it is really hard to understand what you're asking.  

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## 2 answers

### Answer by username_5 on 2017-06-21. Score: 2

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](http://biorxiv.org/content/early/2016/12/07/092304) as an example of how this can be done.

I hope this helps. :)


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### Answer by username_6 on 2017-06-21. Score: 2

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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