I Was Studying A Gene But It Disappeared In The Latest Ensembl Release. What Should I Do Now?

Question

[Giovanni M Dall'Olio]

I am studying a set of genes involved in the same pathway, but this week, after looking at the new release of ensembl, I discovered that the gene was removed. What should I do now? There are references to this gene in several articles and the fact that it disappeared intrigues me - to which sequence these articles were referring to? Is it possible that the ensembl's curators have made an error?

Cheers

[Giovanni M Dall'Olio]

update: the genes have reappeared in the latest Ensembl version.

Answer 1

[Ewan Birney]

Do inform Ensembl via [e-mail]; if it is an error then the Havana curators can put this back in. Send them the ENSG number from the previous release, or the protein sequence, or a page from the archive site. If they think it should have been removed, they will give you a good reason.

[Fred Fleche]

I totally agree and in general the best way to solve such a problem is to contact the helpdesk service dedicated to the given database your are using. In general there are very responsive (e.g. The COSMIC team at Sanger).

Answer 2

[Darked89]

1. Keep on using Ensembl Archive: http://www.ensembl.org/info/website/archives/index.html
2. There is no general answer to question "is gene X real one or it is an artifact removed from Ensembl".
3. You may check i.e. ESTs if they assemble into sensible transcript /compare few species on the genomic level watching for pseudogenes.

Answer 3

[Istvan Albert]

The best course of action would be to contact the people (curators) who made the decision of removing that gene. Keep us posted on what they say, it might be an interesting tidbit about data evolution inside databases ;-0

[Giovanni M Dall'Olio]

they merged it with another gene, with a similar name. Now, there is a gene in ensembl with three transcripts, two of which are localizated in the nucleus and are ribonucleoproteins, and the other is in the ER and catalyze a completely different reaction.

Answer 4

[Steve Moss]

Putting aside questions about annotation; could you not use the previous release of the database, with the gene you were studying? You can define the version to use as part of the API or access previous releases from the website here: http://www.ensembl.org/info/website/archives/index.html. In MySQL if you do a show databases; it also gives you a list of databases you can use, if you prefer to access things from the MySQL client

[Steve Moss]

In the first instance you can use the contact us link, I believe on the site help page or email [e-mail]. You can view the evidence for the assembly and genebuild via the website also, which could possibly give some insight into the reason behind the gene being removed. As with most data, you are generally putting your trust in the programs and methods used for the automated annotation. There are always trade offs between speed and accuracy when automating tasks like these!

[Giovanni M Dall'Olio]

thank you very much for the answer. I can use the older version, but I was just surprised by the fact that they had removed the gene in the newer one. I was wondering how can I know why they did that and how can I inform them that I disagree :-)