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<p>Dear Emily,</p>
<p> </p>
<p>Thank you very much for your time and your important help.</p>
<p> </p>
<p>Best regards,</p>
<p>Michael</p>
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<div style="DIRECTION: ltr" id="divRpF225175"><font color="#000000" size="2" face="Tahoma"><b>From:</b> dev-bounces@ensembl.org [dev-bounces@ensembl.org] on behalf of Emily Pritchard [emily@ebi.ac.uk]<br>
<b>Sent:</b> 21 February 2013 15:20<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] release 70 - Question about Ensembl Data regarding human gene PIK3CG and transcript PIK3CG-001 - References requested<br>
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<div><span style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; DISPLAY: inline !important; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; FLOAT: none; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">Hi Michael</span><br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<span style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; DISPLAY: inline !important; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; FLOAT: none; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">There is information
about Ensembl variation in our documentation, which you'll find here:</span><br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<span style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; DISPLAY: inline !important; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; FLOAT: none; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px"><a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/variation/index.html" target="_blank">http://www.ensembl.org/info/docs/variation/index.html</a></span><br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<span style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; DISPLAY: inline !important; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; FLOAT: none; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">For each gene or
transcript, you can find external references, showing that gene or protein in other databases, some of which are manually curated and have links to publications. For example here are the pages for your gene and transcript of interest:</span><br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<span style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; DISPLAY: inline !important; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; FLOAT: none; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px"><a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Gene/Matches?g=ENSG00000105851;r=7:106505723-106547590" target="_blank">http://www.ensembl.org/Homo_sapiens/Gene/Matches?g=ENSG00000105851;r=7:106505723-106547590</a></span><br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<span style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; DISPLAY: inline !important; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; FLOAT: none; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px"><a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000105851;r=7:106505723-106547590;t=ENST00000440650" target="_blank">http://www.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000105851;r=7:106505723-106547590;t=ENST00000440650</a></span><br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<span style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; DISPLAY: inline !important; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; FLOAT: none; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">You can find variants
within your gene or transcript of interest by going to the Variation table, or by highlighting variants within the sequence (eg gene, exons, cDNA). You can then click on your variant of interest to go to the variant tab:</span><br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<span style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; DISPLAY: inline !important; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; FLOAT: none; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px"><a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Variation/Summary?db=core;g=ENSG00000105851;r=7:106505723-106547590;t=ENST00000440650;v=rs199845412;vdb=variation;vf=54512601" target="_blank">http://www.ensembl.org/Homo_sapiens/Variation/Summary?db=core;g=ENSG00000105851;r=7:106505723-106547590;t=ENST00000440650;v=rs199845412;vdb=variation;vf=54512601</a></span><br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<span style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; DISPLAY: inline !important; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; FLOAT: none; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">From here you can
explore aspects of this variant, for example its source, and external data (such as SNPedia) and population genetics.</span><br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<span style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; DISPLAY: inline !important; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; FLOAT: none; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">In future please
direct all such queries only to helpdesk, not to helpdesk and dev.</span><br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<span style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; DISPLAY: inline !important; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; FLOAT: none; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">Hope this helps,</span><br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<span style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; DISPLAY: inline !important; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; FLOAT: none; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">Emily</span><br style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">
<span style="WIDOWS: 2; TEXT-TRANSFORM: none; TEXT-INDENT: 0px; DISPLAY: inline !important; FONT: 12px Arial,Verdana,sans-serif; WHITE-SPACE: normal; ORPHANS: 2; FLOAT: none; LETTER-SPACING: normal; COLOR: rgb(34,34,34); WORD-SPACING: 0px">Ensembl helpdesk<br>
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<div class="moz-cite-prefix">On 21/02/2013 14:00, M. Diamantidis wrote:<br>
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<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">Dear Ensemble Database,
</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB"></span> </p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">My name is Dr. Michael D. Diamantidis, MSc, PhD. I am a haematologist and working at Erasmus MC, at the haematology department conducting a post doc.</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB"></span> </p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">The release number of the Ensembl version i used and i am posing the question is release 70.</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB"></span> </p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">My question involves Ensembl data.</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB"></span> </p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">I am investigating PIK3CG mutations.</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB"></span> </p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">I would like to ask you to provide me with the possible references regarding the human transcript PIK3CG-001 in two positions.</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB"></span> </p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">The first position i am interested is in exon 2, amino acid 514, which is ATG (Methionine), which has a capital R on top of A, meaning that A or G could occur in the same position.
If G occurs, then the aminoacid in this position is GTG (Valine). I would like to ask if this is a known somatic mutation or a polymorphism (SNIP), what is the relative reference and in which organ this possible mutation occured (tissue sample) - if known.
(Was it large intestine, lung, breast, etc?)</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB"></span> </p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">The second position is in exon 7, amino acid 849, which can be either arginine (CGA) or glutamine (CAA), since there is also an R on top of the base G. I would also like to ask
if this is a known somatic mutation or a polymorphism (SNIP), what is the relative reference and in which organ this possible mutation occured (tissue sample) - if known. (Was it large intestine, lung, breast, etc?)</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB"></span> </p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">I can see that there are also 69 known reported mutations for PIK3CG gene harboring several organs. Could you provide me with the relative references, if possible? Is this material
published or informal and unpublished, but just reported to your site?</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB"></span> </p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">Thank you in advance for your time. I am kindly waiting for your help and answer. I am indebted.</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB"></span> </p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">Yours, sincerely</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB"></span> </p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">Dr. Michael D. Diamantidis, MSc, PhD</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">Haematologist</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">Erasmus MC - Haematology Dept. - Faculty of Medicine</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt">Dr. Molewaterplein 50<br>
3015 GE, Rotterdam <br>
the Netherlands</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">tel: +31 (0) 10 70 38 852</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">fax: +31 (0) 10 70 44 745</span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB">emails:
</span><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt"><a href="mailto:m.diamantidis@erasmusmc.nl" target="_blank"><span lang="EN-GB">m.diamantidis@erasmusmc.nl</span></a></span><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt" lang="EN-GB"></span></p>
<p><span style="FONT-FAMILY: Tahoma; COLOR: black; FONT-SIZE: 10pt"><a href="mailto:diamantidis76@gmail.com" target="_blank"><span>diamantidis76@gmail.com</span></a></span></p>
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<pre class="moz-signature" cols="72">--
Dr Emily Pritchard
Ensembl Outreach Officer
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK </pre>
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