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Get gene ids from probe ids (my idea is right or wrong)

Hi,

I know that there have been multiple suggestions for getting gene ids. I have used a method to do it myself and this is just a post to see if I am doing it right. I have the oligonucleotide probe ids for a set of transcription factors and genes which are part of the Apis Mellifera gene regulatory network. What I did was:

1) I went on GEO and retrieved the sequences for the probes.

2) I further went on NCBI and used BLAST to match these probe sequences with all the sequences in the database related to Apis Mellifera

3) Further, I extracted the ENTREZ IDs of all the hits in an excel sheet.

4) I converted the ENTREZ IDs for all the hits into UNIPROT IDs on UNIPROT.

5) I further, used these UNIPROT IDs to do a functional annotation analysis on DAVID.

Please advice if the methodology I followed was correct and if not, please suggest any changes that I should make to it.

probe blast uniprot entrez david
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written by The Last Word The Last Word

1 answer

So, basically, since there could be a number of hits for a sequence potentially leading to unwanted results, I found a list mapping the probes with their ENTREZ ids and used that for Analysis on DAVID. If you have no option other than using sequences of probes, I would suggest using MEGABLAST to minimize matches. This worked for me and there were only minimal matches per sequence, but I figured that using the ENTREZ ids would be a better option for me. Another suggestion which I received and would like to share is to be careful about using Excel. Because Excel could potentially change ids. Hope these suggestions help you with your research.

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written by The Last Word The Last Word

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