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5.0 years ago
aronsimko
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20
Hi Everyone Just finished a proteomic analysis in cherry and the draft proteome uses identifiers similar to this: "Pav_sc0003434.1_g150.1.mk". I was hoping to do some gene ontology analysis similar to cucumber which i performed previously. I cant find any annotated GO terms for these identifiers,I have over 700 of them to analyse, not sure how to do that "in bulk". Anyways, I was hoping there was a way for me to find orthologs in A. thaliana. I found this paper : https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.13723 , and they mention finding orthologs of N. benthamiana in Arabidopsis however they omit their methods.
Does anyone have experience doing something like this?
You need to retrieve the sequences and then use them as input in GO tools. To find orthologs in arabidopsis just do a blast search and keep the top hits as orthologs. You can try agriGO to get GO terms using corresponding Arabidopsis IDs. agriGO has an option to map sequences from non-model plants on to model plant ids which you can then use as input in agriGO itself.
Thanks. Is there a way to work around retrieving all sequences? I have about 700 or more that i would need to retrieve.
I think you will have to retrieve all sequence if you want GO terms for all of them. After getting the GO terms you can apply a cutoff based on the significance test to filter enriched significant terms. If you have any other data such as expression or interaction data, you can choose sequences of your interest based on that data.
Hi Ashish I appreciate the replies! I decided to only get the GO terms for the most significant changed proteins which lowered the number of sequences i needed to retrieve