Conversion of old gene names into current ones
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Matthias Meyer-Bender
Mar 24, 2021, 1:04:24 PM3/24/21
to gen...@soe.ucsc.edu
Hi,
my name is Matthias and I have a question regarding the conversion of a gene to its symbols. Several years ago, a colleague of mine created a gene reference using hg19, which I am currently updating to hg38. To compare the two, I need to convert some of the old symbols into the new ones. During this process, one particular example came up: in the old reference, there is a gene called LOC283867. I have concluded that this gene has been renamed to LINC00922, however I can not find the old name as an alias anywhere. What I need would be a file to help me convert LOC283867 to LINC00922, but I can not figure out where the description LOC283867 stems from in the first place.
Could you please tell me where this identifier comes from or point me to some resources which might help in this case?
Thank you very much for your help.
Best regards
Matthias
Brian Lee
Mar 24, 2021, 3:56:24 PM3/24/21
to Matthias Meyer-Bender, gen...@soe.ucsc.edu
Dear Matthias,
Thank you for using the UCSC Genome Browser and your question about mapping older hg19 gene names onto current hg38 ones.
One of our engineers recommends the HUGO Gene Nomenclature Committee (HGNC) resource: https://www.genenames.org/
It does look like the specific identifier you mention is not available at HGNC: https://www.genenames.org/tools/search/#!/all?query=LOC283867
A search on our hg19 genome browser turns up this result (a similar search could be done on hg38):
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=LOC283867
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=LOC283867
BC104447 - Homo sapiens hypothetical protein LOC283867, mRNA (cDNA clone IMAGE:40023316).
This helped identify that this goes back to a GenBank source, https://www.ncbi.nlm.nih.gov/nuccore/BC104447?report=GenBank, where you can see after the "ORIGIN" there are was a source mRNA sequence that led to this item, which would help explain why the item is not in HGNC. It will help to learn how the hg19 UCSC Genes Track is different from other tracks (http://genome.ucsc.edu/FAQ/FAQgenes.html#hg19), where it was built with a gene predictor developed at UCSC and likely deemed LOC283867 a potential gene, and referenced the name to the source mRNA. So some of your hg19 gene symbols will not convert into new ones on hg38 as we started using the GENCODE annotations with the new hg38 build.
You might find some of our archived answers on the topic also of interest where we have assisted others in transitioning from the hg19 transcript set to the hg38 transcript set:
https://groups.google.com/a/soe.ucsc.edu/g/genome/search?q=knownGene%20hg19%20hg38
https://groups.google.com/a/soe.ucsc.edu/g/genome/c/mAHLkKs7DU0/m/5gAxGKvJBwAJ
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
Thank you for using the UCSC Genome Browser and your question about mapping older hg19 gene names onto current hg38 ones.
One of our engineers recommends the HUGO Gene Nomenclature Committee (HGNC) resource: https://www.genenames.org/
It does look like the specific identifier you mention is not available at HGNC: https://www.genenames.org/tools/search/#!/all?query=LOC283867
A search on our hg19 genome browser turns up this result (a similar search could be done on hg38):
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=LOC283867
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=LOC283867
BC104447 - Homo sapiens hypothetical protein LOC283867, mRNA (cDNA clone IMAGE:40023316).
This helped identify that this goes back to a GenBank source, https://www.ncbi.nlm.nih.gov/nuccore/BC104447?report=GenBank, where you can see after the "ORIGIN" there are was a source mRNA sequence that led to this item, which would help explain why the item is not in HGNC. It will help to learn how the hg19 UCSC Genes Track is different from other tracks (http://genome.ucsc.edu/FAQ/FAQgenes.html#hg19), where it was built with a gene predictor developed at UCSC and likely deemed LOC283867 a potential gene, and referenced the name to the source mRNA. So some of your hg19 gene symbols will not convert into new ones on hg38 as we started using the GENCODE annotations with the new hg38 build.
You might find some of our archived answers on the topic also of interest where we have assisted others in transitioning from the hg19 transcript set to the hg38 transcript set:
https://groups.google.com/a/soe.ucsc.edu/g/genome/search?q=knownGene%20hg19%20hg38
https://groups.google.com/a/soe.ucsc.edu/g/genome/c/mAHLkKs7DU0/m/5gAxGKvJBwAJ
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
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