Hi friends,
As a result of proteomics (LC MS/MS) of Arabidopsis thaliana leaves, I have more than 1000 identified Proteins. But I just need to work with some groups (for example defensive proteins) so, I am looking for a way by which I can classify the whole proteom functionally. Otherwise, I have to search for protein functions one by one that is very time consuming. So, I need a software or even website by which for instance I can upload the whole proteom sequence, then download a functional classification.
Actually, I don't need just a short annotation describing just the name and location of proteins, since I have them. I specifically need group classification based on function.
I would appreciate for your guide, even if you know any good publication providing a list of defensive proteins in Arabidopsis Thaliana,
Hey Zahra,
have a look at the EggNOG Database (http://eggnogdb.embl.de/#/app/home). This is a database of orthologous groups and functional annotation. On the website you are able to search for annotated orthologous groups of your proteins in other organisms.
Further I would suggest you to search for your proteins at the KEGG Orthology Database (http://www.genome.jp/kegg/ko.html)
Hi Zahra,
For proteomics data analysis you can use DAVID (https://david.ncifcrf.gov), it's easy to use and you can get GO for Function or whatever you are interested on.
I hope that this is useful, all the best
Martin
Just use the IDs and you can get gene ontology here
https://www.arabidopsis.org/tools/go_term_enrichment.jsp
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