I am working on plant proteomics and I have identified more than 4k proteins in different stages, I want to do GO enrichment for all the proteins identified, I tried String but its limit is 2k, I also tried Blast2Go it wasn´t helpful, I tried GoAnna, eggnog mapper, but non of them was helpful in my case. your precious suggestions will be cordially appreciated regarding GO enrichments for higher number of proteins. Thanking in advance.
Hi Sheher Yar,
Have you done a statistical comparison between your stages and get back 4K of differentially expressed proteins? Or are the 4K proteins the total number of all proteins identified in different stages?
To me it doesnt makes much sense to do an enrichment analysis with all identified proteins (except checking for methodological biases).
If you havnt done it already I would suggest to run a simple statistical comparison between your stages and do an enrichment with the differentially expressed proteins only.
Good luck!
Murat
Hi Sheher,
For that, you can use http://www.pantherdb.org/
1. Introduce your gene list
2. Select your species; if you don't find it, you can use a phylogenetically close species
3. In the selection of analysis, a nice visualization option is Functional classification viewed in graphic charts and there pick: Pie chart
4. After that, you will be able to select an ontology among molecular functions, biological processes, pathways etc.
I hope it helps!
Hi Sheher Yar,
You can use panther as suggested by Alexandro Rodríguez-Rojas. You can also try ShinyGo. In case you are working with arabidopsis, you can use AgriGo2.
Cheers,
Dharmesh
Murat Eravci yeah I have already did the statistical analysis, the differentially expressed proteins analysis is also a good idea, but i was thinking if its possible to do for all the proteins of different stages. thanks a lot for your precious suggestion.
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