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5.7 years ago
The Last Word
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I have a bunch of beebase ids. Which converter can i use to convert them to Uniprot ids? Beebase as it is, is a poorly maintained database. Example of the ids are
GB12498
GB16677
GB16154
GB18362
GB30528
GB16592
GB12455
GB30150
GB17048
GB17763
Provide examples of the said ID's.
@genomax please see the edit
Looks like you can use the HymenopteraMine to recover the info you need. Tutorial here.
I tried this before. Sadly, HymenopterMine doesn't work and is not well maintained.
For this query you may have to do the mapping yourself by using original sequences, if the BeeBase is not actively maintained and you have not found alternate means to get this information.
Hi genomax, I think I found the problem. These ids are from official gene set v1.0 for apis mellifera. The latest geneset is OGS3.2. Hymenopteramine is tuned to retrieve ids from only this new dataset. I found a paper that mapped these gene ids to the new geneset and they say they used BLAST but I can't seem to understand how they did that. This is the paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275039/
I see that the BEEBASE ID's in latest GTF file contain none of the ID's you have posted above.
I see a number of arrays listed in EBI Array Express. You can look through these to see which of them matches the ID's you have, which should give you sequence of the oligos for those ID's. I think you will need to take those sequences and use blast against the current genome build to identify current BeeBase ID's.
EDIT: I found the excel file that contains the oligo sequences for the ID's you have, along with the ADF file.
I wanted to ask a question. Here is another oligonucleotide array https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16023 with sequences for the beebase IDs. The sequences in the set that you gave earlier and the ones in this are different. Any idea why that would be the case. I was actually using the former to retrieve the sequences of the probes. Might be a stupid question but my knowledge with microarray analysis is limited.
As you saw from the EBI Array Express link there were multiple versions/types of Apis arrays. This is a good illustration of how messy things become without proper metadata. The link for the excel file was from 2010 where as the platform link you included is from 2012 that must be a newer iteration.
Do you know which array/data your ID's originate from? That would really be the only way to nail this down for sure.
I am actually working on this network https://hood-price.systemsbiology.org/research/honeybee-transcriptional-regulatory-network/ . The paper linked to it is https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755009/ . I did reread the paper for this information but other than stating that the brain transcriptome data set was generated in Dr. Robinson’s lab. I couldn't find any information about the platform used.
Found it Genomax. Its https://www.ebi.ac.uk/arrayexpress/arrays/A-MEXP-755/?ref=E-TABM-953 . In that paper, in the methods section, he has mentioned some other studies done on the same array. Thank you for your help and guidance.