gene naming

Question

[sasogalaxy90]

Hi all,

I hope someone can advise me regarding this issue, I'm performing RNA-seq experiments and DEseq2 analysis, some of the detected genes had Ensemble IDs but no gene name (symbol), I contacted zfin nomenclature team and submitted nomenclature proposal to the most similar gene sequence (in blast results). my question is if this is something to mention when publishing those data and how to document it?

[dthorbur]

For publications, I will assign orthologs to a better annotated species (for example, the zebrafish for my work in stickleback), and if they have a gene name that is what I'll report. If not, I'll use the ensembl gene name. Something like "XCR1A, NXPE3, and an unnamed gene (ENSGACG00000011711)"

As long as it's traceable, I don't think you'll have a problem. But, when you are inheriting names from orthologous sequences, please provide the original ensmebl gene name in a supplementary table.

[sasogalaxy90]

thank you for your answer, I forgot to mention that I work with zebrafish which is well annotated species but some detected genes are still unnamed yet and assigned in ensemble database as "Novel genes", so do you think I can also name them "novel genes" in my publication or not since those genes are already identified and given ensemble IDs?

[dthorbur]

I would look into why Ensembl are calling them novel before calling them that in a publication. What is novel about them? Is it that they have only recently been classified in Zebrafish? I would ask for evidence of why they are being called novel if I was a reviewer.

Answer 1

[Kevin Blighe]

You simply report that they have no known gene symbol, i.e., you report it as NA.

It is perfectly normal that many genes with an Ensembl ID will not have a corresponding gene symbol.

Kevin

[sasogalaxy90]

thank you for your comment. but how should I document this if I already submitted nomenclature proposal for them and names approved. so they are named

[GenoMax]

If you have received Ensembl names approval (that you have documentation for) then you could use them with a note that as of date when you submit the paper they are not live on Ensembl web site.