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[go-helpdesk] Multiple results for single human gene name

Tanya Berardini tberardi at acoma.stanford.edu
Fri Jun 15 15:08:43 PDT 2012


Dear Peter,

The most conservative way to obtain all of the annotations for your genes
of interest, regardless of UniProt ID and associated a.a. length or record
contents, is to just use the union of all annotations for all UniProt IDs
associated with that gene name.  For the example you sent yesterday, this
would mean taking all the annotations for all six records that were
returned in your search.

HGNC numbers can be used to search GO but they too do not return a single
record as one HGNC number can be associated to several UniProtKB
identifiers. (I tried an exact search for HGNC:HGNC:50 which gave me 161
results!)

I hope this information helps.

Best wishes,


Tanya

On Fri, Jun 15, 2012 at 3:28 AM, Peter Stenson <StensonPD at cardiff.ac.uk>wrote:

>
> Dear Tanya
>
> Thank you for your reply.
>
> My goal is to be able to produce a list of ontology terms associated with
> a gene (not a protein or protein fragment).
>
> Since UniProt catalogues proteins not genes, how should I uniquely
> identify a gene in AmiGO without resorting to calculating protein lengths
> from UniProt, and using the longest one, or relying on the most extensive
> record in the database as being the one to use?
>
> I guess I am asking if there is a list of unique gene identifiers (e.g.
> HGNC numbers) in GO?
>
> Many thanks
>
> Best regards
>
> Peter
> HGMD
>
>
>
>
> -----tberardi at arabidopsis.org wrote: -----
> To: stensonpd at cardiff.ac.uk
> From: Tanya Berardini **
> Sent by: tberardi at arabidopsis.org
> Date: 06/13/2012 07:02PM
> Cc: gohelp <go-helpdesk at lists.stanford.edu><go-helpdesk at lists.stanford.edu>,
> software-group <software-group at genome.stanford.edu><software-group at genome.stanford.edu>
> Subject: Multiple results for single human gene name
>
>
> Dear Peter,
>
> Thank you for contacting GO with your question.  The six different human
> WHSC1 results in AmiGO correspond to six different UniProtKB records that
> are all called WHSC1. If you click on each name, you will see that the
> links to UniProtKB are all different.
>
> Four of them have this tag:
>
> "The sequence shown here is derived from an Ensembl automatic analysis
> pipeline and should be considered as preliminary data. "
>
> http://www.uniprot.org/uniprot/D6R9V2
> http://www.uniprot.org/uniprot/D6RFE7
> http://www.uniprot.org/uniprot/D6RIS1
> http://www.uniprot.org/uniprot/H0Y9U6
>
> The remaining two differ in the length of the amino acid sequence.
>
> http://www.uniprot.org/uniprot/O96028
> http://www.uniprot.org/uniprot/A2A2T2
>
>
> Depending on your goals, you may want to focus on just one or several of
> these records.  This one, http://www.uniprot.org/uniprot/O96028, is the
> longest amino acid sequence and appears to be the most extensive record.
> If you use this UniProtKB identifier in your AmiGO search, you will only
> get one result.
>
> Best wishes,
>
>
> Tanya Berardini
>
>
> ---------- Forwarded message ----------
> From: stensonpd at cardiff.ac.uk
> To: go-helpdesk at mailman.stanford.edu
> Cc:
> Date: Wed, 13 Jun 2012 02:50:49 -0700
> Subject: GO Help query (from website)
>
> Email: stensonpd at cardiff.ac.uk
> Name: Ontology (from Peter Stenson)
> Text: Hello
> I am having trouble uniquely identifying genes in the GO database (online
> and download).
>
> For example, the search for human WHSC1 (
> http://amigo.geneontology.org/cgi-bin/amigo/search.cgi?search_query=whsc1&search_constraint=gp&exact_match=1&session_id=5535amigo1339580308&action=new-search)
> brings up 6 results, all of which seem to be pointing to the same gene. Can
> you explain why there are 6 entries here, rather than just 1? Many thanks.
>
>
> **
>
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