[ensembl-dev] Annotation discrepancy

[ian Longden]

150000, 51275, 55449, 57126,  503646, 8693 are all unmapped in human.
These will have entrys in the xref table but are not linked to any genes.
I am not sure how the search is done but this may affect it.

984:-
Not sure what the problem is here we find the genes of interest but
this gene also has other EntrezGene ids.

8857:-
as above

9026:-
as above.

Were you expecting only 1 EntrezGene per gene? In time i hope this
becomes true but as these are very similar the software cannot choose
between them and uses both.

I think the data is correct but maybe the search is not giving you
exactly what you want.
We need to look at having the unmapped cases searchable.

0Ian.

On Fri, Nov 19, 2010 at 11:55 AM, Oliver, Gavin
<gavin.oliver at almacgroup.com> wrote:
> I have a few more examples of discrepancies which will hopefully help.
>
>
>
> For all examples, the search was performed on Entrez ID but returned
> nothing.  I have looked a bit deeper into a handful of examples.  Details
> below:
>
>
>
> Entrez ID 150000           Associated gene Symbol ABCC13 in database but
> with no associated entrez ID
>
> Entrez ID  51275            Associated gene symbol C12orf47 in database but
> no associated entrez ID
>
> Entrez ID  55449            Associated gene symbol C14orf167 in database but
> no associated entrez ID
>
> Entrez ID  57126            Associated gene symbol CD177 in database with no
> associated entrez id
>
> Entrez ID  984               Associated gene symbol CDK11B is not in
> database.  CDK11A is in database but is annotated as cyclin-dependent kinase
> 11B with entrez id 100294398 which entrez describes as LOC100294398 (cell
> division protein kinase 11B-like).
>
> Entrez ID  503646          Neither this ID nor associated gene symbol DPRXP5
> are in the database.
>
> Entrez ID  8857              Associated gene symbol FCGBP (Fc fragment of
> IgG binding protein) is there but with Entrez gene ID 100133944 which
> corresponds to LOC100133944 IgGFc-binding protein-like.
>
> Entrez ID  8693              Neither this ID nor associated gene symbol
> GALNT4 are in the database.
>
> Entrez ID  9026              Gene symbol HIP1R (huntingtin interacting
> protein 1 related) is in the database but with entrez ID 100294412 which
> corresponds to huntingtin-interacting protein 1-related protein-like
>
>
>
> Best,
>
>
>
> Gavin
>
>
>
>
>
>
>
> ________________________________
>
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of
> Oliver, Gavin
> Sent: 19 November 2010 10:29
> To: dev at ensembl.org
> Subject: [ensembl-dev] Annotation discrepancy
>
>
>
> Hi all,
>
>
>
> I have been using Ensembl human for internal annotation of microarrays.
>
>
>
> Yesterday someone did a search for Entrez Gene ID 3336 in our database.  It
> returned no hits.
>
>
>
> When they searched with the Gene symbol for this ID (HSPE1), they got 5 hits
> but the Entrez ID associated with the gene was 100132346 (and not 3336 as
> would be expected).
>
>
>
> I ran a search for 100132346 against the Ensembl genome browser and it
> brings back 2 genes on 2 different chromosomes.
>
>
>
> Can someone explain what might be happening here?
>
>
>
> Best,
>
>
>
> Gavin
>
>
>
>
>
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