[ensembl-dev] thank you - RE: release 70 - Question about Ensembl Data regarding human gene PIK3CG and transcript PIK3CG-001 - References requested

Thu Feb 21 16:06:17 GMT 2013

Dear Emily,

Thank you very much for your time and your important help.

Best regards,

Michael

________________________________
From: dev-bounces at ensembl.org [dev-bounces at ensembl.org] on behalf of Emily Pritchard [emily at ebi.ac.uk]
Sent: 21 February 2013 15:20
To: Ensembl developers list
Subject: Re: [ensembl-dev] release 70 - Question about Ensembl Data regarding human gene PIK3CG and transcript PIK3CG-001 - References requested

Hi Michael

There is information about Ensembl variation in our documentation, which you'll find here:
http://www.ensembl.org/info/docs/variation/index.html

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:
http://www.ensembl.org/Homo_sapiens/Gene/Matches?g=ENSG00000105851;r=7:106505723-106547590
http://www.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000105851;r=7:106505723-106547590;t=ENST00000440650

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:
http://www.ensembl.org/Homo_sapiens/Variation/Summary?db=core;g=ENSG00000105851;r=7:106505723-106547590;t=ENST00000440650;v=rs199845412;vdb=variation;vf=54512601

>From here you can explore aspects of this variant, for example its source, and external data (such as SNPedia) and population genetics.

In future please direct all such queries only to helpdesk, not to helpdesk and dev.

Hope this helps,

Emily
Ensembl helpdesk

On 21/02/2013 14:00, M. Diamantidis wrote:

Dear Ensemble Database,

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.

The release number of the Ensembl version i used and i am posing the question is release 70.

My question involves Ensembl data.

I am investigating PIK3CG mutations.

I would like to ask you to provide me with the possible references regarding the human transcript PIK3CG-001 in two positions.

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?)

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?)

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?

Thank you in advance for your time. I am kindly waiting for your help and answer. I am indebted.

Yours, sincerely

Dr. Michael D. Diamantidis, MSc, PhD

Haematologist

Erasmus MC - Haematology Dept. - Faculty of Medicine

Dr. Molewaterplein 50
3015 GE, Rotterdam
the Netherlands

tel: +31 (0) 10 70 38 852

fax: +31 (0) 10 70 44 745

emails: m.diamantidis at erasmusmc.nl<mailto:m.diamantidis at erasmusmc.nl>

diamantidis76 at gmail.com<mailto:diamantidis76 at gmail.com>

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--
Dr Emily Pritchard
Ensembl Outreach Officer

EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK
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