Question: Is there any resource annotating protein function within a pathway?
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gravatar for ajingnk
4.6 years ago by
ajingnk120
United States
ajingnk120 wrote:

We can easily find whether the protein is in certain pathway. But, is there any role annotation of proteins in pathways? Because, one protein may act as different roles in different pathways. This is probably related to semantic net for the biological process within a cell or system biology.

protein pathway • 1.2k views
ADD COMMENTlink modified 12 weeks ago by Biostar ♦♦ 20 • written 4.6 years ago by ajingnk120
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gravatar for emekdemir
4.6 years ago by
emekdemir100
United States
emekdemir100 wrote:

Hi,

Would pathwaycommmons.org webservices would help?

Also would you elaborate a bit more on your use case? What do you expect in terms of the  "role annotation" ? A controlled vocabulary term? What would be some example terms?

 

Best,

ED

 

 

ADD COMMENTlink written 4.6 years ago by emekdemir100

I was thinking about whether proteins playing the same role in a pathway will have similar structure properties (like size of protein, protein binding sites, and so on).  I am not sure whether this is a valid question. Some proteins could be activator, inhibitor, or substrate. 

The pathway common website is really great. The annotation of edges could be treated like the role for the relationship. But, for here, mostly are "changes the state" and this is only for genes.

ADD REPLYlink written 4.6 years ago by ajingnk120
0
gravatar for emekdemir
4.6 years ago by
emekdemir100
United States
emekdemir100 wrote:

What you are exploring is a simplified view, geared toward mostly genomic use-cases - PC contains detailed information about the actual reactions between proteins. You can use Chibe to fully explore them: http://www.biomedcentral.com/1471-2164/15/642

As with the protein structure properties I am not sure about the roles but phosphorylation sites of different proteins tend to have some property similarities but the signal is not very strong in my experience.

ADD COMMENTlink written 4.6 years ago by emekdemir100
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