<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<tt>Dear Souhila,<br>
</tt><tt><tt>Defining a specific cutoff score is not very easy, as
this is something that varies across cell types.<br>
Since we are focused on potential binding within our predicted
regulatory elements, we set a non strict p-value in the
detection algorithm that we used so that we wouldn't miss
potentially interesting sites.<br>
As a result the reported match score can be quite varied among
motif features.<br>
<br>
Kind Regards,<br>
Ilias<br>
<br>
<br>
<br>
<br>
</tt></tt>
<div class="moz-cite-prefix">On 30/04/2020 18:00, Souhila
Amanzougarene wrote:<br>
</div>
<blockquote type="cite"
cite="mid:20200430170146.52B0313447A_EAB047AB@hx-mx2.ebi.ac.uk">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<p><tt>Hi Anja, </tt><tt><br>
</tt></p>
<p><tt>Thanks a lot for your response. <br>
</tt></p>
<p><tt><tt>I understand. </tt>Yes, I wanted to get taget gene
that is regulated by a given motif feature. </tt><tt><br>
</tt></p>
<p><tt>I have another question about </tt><tt><span itemscope=""
itemtype="http://schema.org/Question"><span itemprop="text">the
<b>motif score change,</b> I don't understand when can we
say that the </span></span></tt><span itemscope=""
itemtype="http://schema.org/Question"><span itemprop="text"><tt>difference
in motif score</tt><tt> is high or low, is there a </tt><tt>threshold
? How to interpret the negatif or positif diffeneces?</tt></span></span></p>
<p><span itemscope="" itemtype="http://schema.org/Question"><span
itemprop="text"><tt><br>
</tt></span></span></p>
<p><span itemscope="" itemtype="http://schema.org/Question"><span
itemprop="text"><tt>Best regards</tt></span></span></p>
<p><span itemscope="" itemtype="http://schema.org/Question"><span
itemprop="text"><tt><br>
</tt></span></span></p>
<p><span itemscope="" itemtype="http://schema.org/Question"><span
itemprop="text"><tt>Souhila<br>
</tt></span></span></p>
<p><span itemscope="" itemtype="http://schema.org/Question"><span
itemprop="text"><b><br>
</b></span></span></p>
<div class="moz-cite-prefix">Le 29/04/2020 à 13:47, Anja Thormann
a écrit :<br>
</div>
<blockquote type="cite"
cite="mid:CA20F870-6D16-40CA-8373-C88F92B451F9@ebi.ac.uk">
<meta http-equiv="Content-Type" content="text/html;
charset=UTF-8">
Dear Souhila,
<div class=""><br class="">
</div>
<div class="">we don’t have any information about the gene that
is regulated by a given motif feature if that is what you were
after. Please let me know if that is not the case. VEP returns
gene IDs for variants which overlap transcripts.</div>
<div class=""><br class="">
</div>
<div class="">Best regards,</div>
<div class="">Anja</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 27 Apr 2020, at 16:35, Souhila
Amanzougarene <<a
href="mailto:souhila.amanzougarene@cnrs.fr" class=""
moz-do-not-send="true">souhila.amanzougarene@cnrs.fr</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div text="#000000" bgcolor="#FFFFFF" class="">
<p class="">Hi Ensembl Developers,</p>
<p class="">I used VEP to annotate vcf files, I'm
interested by the <b class="">MotifFeature</b>. In
the annotated file, I have only the ensembl motif ID
(Feature column). <br class="">
</p>
<p class="">Is there any way to get gene ID in
addition of the ensembl motif ID.</p>
<p class="">Best regards<br class="">
</p>
<pre class="moz-signature" cols="72">--
Souhila Amanzougarene</pre>
</div>
_______________________________________________<br
class="">
Dev mailing list <a href="mailto:Dev@ensembl.org"
class="" moz-do-not-send="true">Dev@ensembl.org</a><br
class="">
Posting guidelines and subscribe/unsubscribe info: <a
href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org"
class="" moz-do-not-send="true">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a><br
class="">
Ensembl Blog: <a href="http://www.ensembl.info/"
class="" moz-do-not-send="true">http://www.ensembl.info/</a><br
class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org" moz-do-not-send="true">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org" moz-do-not-send="true">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/" moz-do-not-send="true">http://www.ensembl.info/</a>
</pre>
</blockquote>
<pre class="moz-signature" cols="72">--
Souhila Amanzougarene
</pre>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</body>
</html>