[ensembl-dev] Many Ensembl-Ids lack annotation?

Ewan Birney birney at ebi.ac.uk
Tue Aug 16 16:33:35 BST 2011


On 16 Aug 2011, at 15:55, Colin Davenport wrote:

> 
> Dear Ensembl users,
> 
> firstly, congratulations. Ensembl is a nice resource which we don't have in the bacterial world!
> 

Au contraire! Check out:

http://bacteria.ensembl.org/index.html

This has been going for about 2 years, but it's fair to say that we've (so far)
had the least traction and impact in bacteria. We (in particular my colleague Paul Kersey and myself)
would be very interested in people's experience of Ensembl bacteria and what could
be done to make it more useful - Paul's email is pkersey at ebi.ac.uk


I'll let the Ensembl experts answer this one.

> I have a question about some very highly expressed genes which are lacking annotations in the current Ensembl database v62.
> 
> I am using the edgeR bioconductor package to analyse human RNA-seq data. Some of the most important genes in the dataset
> have Ensembl IDs, but no annotation attached (see examples below, eg. ENSG00000257107).
> 
> Are these old, too new or am I missing something here?
> 



> If I look up the gene on the Ensembl website I get. (IDHistory_gene)
> Ensembl gene ENSG00000257107 is no longer in the database and has not been mapped to any newer identifiers
> 
> In fact, the edgeR ensembl database has about 52000 entries, but the bioMart export only gives me about 22000 entries with annotation.
> Surely at least the important highly expressed genes must have been mapped to other identifiers if they have been removed ?
> 
> 
> 
> 
> Thanks for any help!
> Regards,
> Colin
> 
> ENSG00000196565	HBG2	11	hemoglobin, gamma G [Source:HGNC Symbol;Acc:4832]
> ENSG00000188536	HBA2	16	hemoglobin, alpha 2 [Source:HGNC Symbol;Acc:4824]
> ENSG00000244734	HBB	11	hemoglobin, beta [Source:HGNC Symbol;Acc:4827]
> ENSG00000206172	HBA1	16	hemoglobin, alpha 1 [Source:HGNC Symbol;Acc:4823]
> ENSG00000257107		
> 
> ENSG00000255592	
> 
> 
> ENSG00000210082	
> 
> 
> ENSG00000211459	
> 
> 
> ENSG00000105372	RPS19	19	ribosomal protein S19 [Source:HGNC Symbol;Acc:10402]
> ENSG00000198712	MT-CO2	MT	mitochondrially encoded cytochrome c oxidase II [Source:HGNC Symbol;Acc:7421]
> 
> 
> 
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