<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="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 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_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/<wbr>Homo_sapiens/Search/Results?q=<wbr>atxn3;site=ensembl_all;page=1;<wbr>facet_feature_type=Gene;facet_<wbr>species=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_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/<wbr>Homo_sapiens/Gene/Matches?db=<wbr>core;g=ENSG00000259634;r=14:<wbr>92523341-92575863;t=<wbr>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="h5"><br>
<br>
<br>
<div class="m_3152206528305677730moz-cite-prefix">On 15/07/2017 12:55, Mahmood Naderan
wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<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_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_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>
<br>
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