<div dir="ltr"><div class="gmail_default" style="font-family:tahoma,sans-serif">Dear Mag,<br></div><div class="gmail_default" style="font-family:tahoma,sans-serif">Regarding your explanation, I understand most of it (as I said before I am not expert in this field) but can you answer this:<br></div><div class="gmail_default" style="font-family:tahoma,sans-serif">What information will be missed if I use fetch_all_by_external_name and what information will be missed if I use fetch_all_by_display_name?<br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><font face="tahoma,sans-serif">Regards,<br>Mahmood</font><br><br><br></div></div></div>
<br><div class="gmail_quote">On Thu, Jul 20, 2017 at 1:01 PM, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
Hi Mahmood,<br>
<br>
We map a large number of external references to Ensembl features.<br>
These can be proteins (eg UniProt), mRNAs (eg RefSeq), non coding
RNAs (RFAM, miRBase), as well as a number of annotations, for
example aberrant sites (DBASS) or pathways (Reactome).<br>
<br>
Some of these have gene symbols associated with them and we use
those links to name our genes. For human, this will generally be
HGNC, as this is the official nomenclature committee.<br>
This means the most trusted, confident link will be used as what we
call the display_xref, to assign the gene name. There might still be
some other links which could be used as gene symbol but are of lower
priority. For example, we can have an HGNC symbol as well as an
EntrezGene link.<br>
<br>
As a result, fetch_all_by_display_name will only use external
references used for the selected naming symbol, usually HGNC, while
fetch_all_by_external_name will query across all external references
associated with the Ensembl gene.<br>
<br>
<br>
Hope that helps,<br>
Magali<div><div class="h5"><br>
<br>
<div class="m_-1110355637117926439moz-cite-prefix">On 20/07/2017 09:21, Mahmood Naderan
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_default" style="font-family:tahoma,sans-serif">Hi
Mag,<br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif">Some
of my questions were answered, though some new questions
arose. For example, what is the difference between
fetch_all_by_external_name and fetch_all_by_display_name. The
descriptions in core document seems to be similar and I can
not find where should I use the first and where should I use
the second.<br>
<br>
</div>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div class="m_-1110355637117926439gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr"><font face="tahoma,sans-serif">Regards,<br>
Mahmood</font><br>
<br>
<br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">On Mon, Jul 17, 2017 at 7:02 PM, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> Hi Mahmood,<br>
<br>
The fetch_all_by_external_name returns a list of genes for
which atxn3 is an associated link.<br>
For GRCh37, there are two genes which qualify, as can be
seen on the search page:<br>
<a class="m_-1110355637117926439m_3152206528305677730moz-txt-link-freetext" href="http://grch37.ensembl.org/Homo_sapiens/Search/Results?q=atxn3;site=ensembl_all;page=1;facet_feature_type=Gene;facet_species=Human" target="_blank">http://grch37.ensembl.org/Homo<wbr>_sapiens/Search/Results?q=atxn<wbr>3;site=ensembl_all;page=1;face<wbr>t_feature_type=Gene;facet_spec<wbr>ies=Human</a><br>
If you check the second element of the list, you will get
ENSG00000066427<br>
<br>
For ENSG00000259634, atxn3 is not the main display name,
but it has a link to the corresponding NCBIgene entry for
atxn3.<br>
<a class="m_-1110355637117926439m_3152206528305677730moz-txt-link-freetext" href="http://grch37.ensembl.org/Homo_sapiens/Gene/Matches?db=core;g=ENSG00000259634;r=14:92523341-92575863;t=ENST00000558190" target="_blank">http://grch37.ensembl.org/Homo<wbr>_sapiens/Gene/Matches?db=core;<wbr>g=ENSG00000259634;r=14:9252334<wbr>1-92575863;t=ENST00000558190</a><br>
<br>
If you are only interested in genes for which atxn3 is the
chosen symbol, you can use the fetch_all_by_display_label
method instead.<br>
<br>
However, please be aware that the
fetch_all_by_display_label will still return a list of
genes, which could have more than one element.<br>
For example, two genes can share the same name if one is
on the reference while the other one is on a haplotype.<br>
There are also cases where a name is misassigned to a
gene, resulting in a duplication. This can happen when two
genes are overlapping.<br>
<br>
Because of this, I would recommend looping through the
resulting list rather than assume the first result is the
one you want.<br>
You can then check for various gene attributes to ensure
this is the one you expect.<br>
<br>
<br>
Hope that helps,<br>
Magali
<div>
<div class="m_-1110355637117926439h5"><br>
<br>
<br>
<div class="m_-1110355637117926439m_3152206528305677730moz-cite-prefix">On
15/07/2017 12:55, Mahmood Naderan wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="m_-1110355637117926439h5">
<div dir="ltr">
<div class="gmail_default" style="font-family:tahoma,sans-serif">I have an
update that may shed a light but I cannot figure
out.<br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif">With the
command in my previous email, I see that the
stableID is ENSG00000259634. As I enter this ID
in the web site, I see <br>
<br>
Gene: RP11-529H20.5 ENSG00000259634 . Location
Chromosome 14: 92,524,896-92,525,877 reverse
strand.<br>
<br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif">As you can
see the start and end numbers matches with my
previous email and its name is not ATXN3 which I
requested in the command. So, the question is
that why fetch_all_by_external_name("at<wbr>xn3")
returns that.<br>
<br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif">In my
previous questions, Emily pointed that function
may returns LRGs. For me it is hard to
understand since I am not an expert in that
field. I want to the get the main gene and not
anything else.<br>
</div>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div class="m_-1110355637117926439m_3152206528305677730gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr"><font face="tahoma,sans-serif">Regards,<br>
Mahmood</font><br>
<br>
<br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">On Sat, Jul 15, 2017 at
2:15 PM, Mahmood Naderan <span dir="ltr"><<a href="mailto:mahmood.nt@gmail.com" target="_blank">mahmood.nt@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div class="gmail_default" style="font-family:tahoma,sans-serif">Hi,<br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif">With
this code<br>
<br>
my @genes = @{
$gene_adaptor->fetch_all_by_ex<wbr>ternal_name("atxn3)
};<br>
my $gene = @genes[0];<br>
my $start = $gene->start();<br>
my $end = $gene->end();<br>
<br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif">I
see that<br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif">
start=92524896<br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif">
end=92525877<br>
<br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif">However,
from the website, I see<br>
Chromosome 14: 92,524,896-92,572,965<br>
<br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif">As
you can see, the end numbers are
different.<br>
<a href="http://grch37.ensembl.org/Homo_sapiens/Gene/Sequence?db=core;g=ENSG00000066427;r=14:92524896-92572965" target="_blank">http://grch37.ensembl.org/Homo<wbr>_sapiens/Gene/Sequence?db=core<wbr>;g=ENSG00000066427;r=14:925248<wbr>96-92572965</a><br>
<br>
<br>
Is there any reason for that?<br>
<br>
</div>
<div>
<div class="m_-1110355637117926439m_3152206528305677730m_8338690354492335674gmail_signature">
<div dir="ltr"><font face="tahoma,sans-serif">Regards,<br>
Mahmood</font><br>
<br>
<br>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
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