Question: How To Get All The Mrna Or Protein Sequences In A Pathway For Fruitfly?
1
gravatar for Dejian
8.3 years ago by
Dejian1.3k
United States
Dejian1.3k wrote:

I want to get all the mRNA or protein sequences in a specific pathway, e.g. glycolysis or oxidative phosphorylation, from fruitfly. Is there a convenient way to attain this goal?

I first thought of KEGG database; however, KEGG pathway does not possess pathways specific for fruitfly. (It seems that kegg pathway only has specific pathways for vertebrates.)

Then I turned to FlyBase and found QueryBuilder help a bit.But I am not sure whether I got all genes and no extra in oxidative phosphorylation for fruitfly by setting the controlled vocabularies to be "oxidative phosphorylation".

I also tried BioMart and failed, because I am not familiar with it. I hope that someone shows me how to do it if BioMart is the right choice.

If there are other tools that can do this job, I would like to try.

Many thanks!

pathway sequence retrieval • 2.2k views
ADD COMMENTlink modified 7.9 years ago by Chris Evelo10.0k • written 8.3 years ago by Dejian1.3k
6
gravatar for Fred Fleche
8.3 years ago by
Fred Fleche4.3k
Paris, France
Fred Fleche4.3k wrote:

[?]

http://www.genome.jp/kegg-bin/show_pathway?org_name=dme&mapno=00190&mapscale=&show_description=hide

ADD COMMENTlink written 8.3 years ago by Fred Fleche4.3k
2

If this is the best answer, you should select it as such and vote for it.

ADD REPLYlink written 8.3 years ago by Neilfws48k

Yes,indeed. I made a mistake. Thank you very much.

ADD REPLYlink written 8.3 years ago by Dejian1.3k
3
gravatar for Bert Overduin
8.3 years ago by
Bert Overduin3.6k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.6k wrote:

Hello,

Reactome contains pathways for fly, but note that these are inferred from human through orthologous relationships.

You can retrieve the genes involved in a Reactome pathway using BioMart. For example, if you want to retrieve the genes involved in glycolysis:

(1) Go to BioMart. Select 'REACTOME (CSHL US)'. Select 'pathway'.

(2) Click on 'Filters' in the side menu. Select 'Limit to species - Drosophila melanogaster'. Select 'Pathway name - Glycolysis'.

(3) Click on 'Attributes' in the side menu. Select the information you want to retrieve, e.g. 'Gene ENSEMBL ID'.

(4) Click the [Results] button. This gives you a preview which consists of the first 10 rows of results. To get the full set of results select 'View all rows' or export your results to a file.

Hope this helps.

ADD COMMENTlink written 8.3 years ago by Bert Overduin3.6k

Thank you very much, Bert. This is a good example to demo how to use BioMart. Additionally, it will help me solve other problems in my project.

ADD REPLYlink written 8.3 years ago by Dejian1.3k
1
gravatar for Chris Evelo
8.3 years ago by
Chris Evelo10.0k
Maastricht, The Netherlands
Chris Evelo10.0k wrote:

WikiPathways does have [?]34 pathways specific for Drosophila Melanogaster[?] including glycolysis and oxidative phosphorylation, and you could add more. The backpages will connect to protein and sequence databases.

You can download the list of genes and proteins directly from the respective pathway pages or use the [?]WikiPathways webservice[?] to do that.

ADD COMMENTlink modified 8.3 years ago • written 8.3 years ago by Chris Evelo10.0k

Thank you for recommending new resources,Chris. But I am dubious about the reliability of wiki-series data for academic researches. Thank you anyway.

ADD REPLYlink written 8.3 years ago by Dejian1.3k

You could be right about the Drosophila pathways specifically, they were originally inferred from human and mice pathways, and then improved by the community. The broader meaning of your comment asks for an answer that doesn't fit in a comment. But if you do find information elsewhere that is not present or wrong in WikiPathways please help to improve them.

ADD REPLYlink written 8.3 years ago by Chris Evelo10.0k
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