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Post by priscillaglenn on Mar 29, 2024 10:02:05 GMT -5
Hi all,
I'm fairly new to GO term analysis and have been analyzing a Sorghum Bicolor experiment (gene list and background) using DAVID. I noticed that some genes that we believe are involved in the clock do not have any Biological Process GO terms. Is there a way to update the GO terms on DAVID or to download/manually redo the analysis with these GO terms included?
Thanks,
Priscilla
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Brad
DAVID Bioinformatics Team
Posts: 67
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Post by Brad on Apr 10, 2024 9:09:02 GMT -5
Hi Priscilla,
Thank you for your question. Do you have some examples genes that you expect to be annotated to clock processes?
Regards, Brad
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Post by sfbello on Apr 16, 2024 6:22:19 GMT -5
Good day, I am trying to do DAVID Bioinformatics on 1544 Ensemble gene ID from Chicken. However, only 38 were listed related to Gallus gallus Please find attached the list of the gene Thank you Ensemble gene ID.xlsx (26.33 KB) |
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Brad
DAVID Bioinformatics Team
Posts: 67
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Post by Brad on Apr 19, 2024 12:34:25 GMT -5
Thank you for providing the list. We base our Ensembl gene id mappings based on NCBI (Entrez) and Uniprot annotation but not the Ensembl data. However, based on Ensembl's data, 332 of your ids have been retired. Ensembl does provide mappings to Entrez Gene Id or Uniprot Accession for most of your other identifiers but typically, Entrez will reference a different Ensembl id (or none) and the Uniprot accession referenced by Ensembl is retired. For instance, the Ensembl entry for ENSGALG00000000081(http://www.ensembl.org/id/ENSGALG00000000081) references Entrez Gene Id 417039 (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=417039) but NCBI references Ensembl ENSGALG00010002669 (http://www.ensembl.org/id/ENSGALG00010002669; same gene but different build). This entry also references Uniprot accession F1NM87 (http://www.uniprot.org/uniprot/F1NM87) which is retired. I am attaching a file using the Ensembl mappings (from Ensembl directly) from your ids to both Entrez gene id and Uniprot accession, either of which may be uploaded to DAVID and should result in a higher percentage of mappings. I hope it is helpful. Regards, Brad Ensemble gene ID.withEntrez_UniprotAccessi....xlsx (51.74 KB)_ |
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