Missing genes?

[kim summers (RI)]

Dear BioGPS team

 

I am trying to find the expression profiles for mouse smooth muscle alpha actin (Acta2). The search function is not finding this gene for the mouse, only human, rat and Drosophila. But I know it is there because I have the data downloaded for mouse. I would really like to see the pattern for this gene - can you see if there is a problem please?

 

Also we have been looking for 2700049A03Rik (probe 1429595_at). We can see this in the raw data but there is no profile. In this case a gene is found but there is no graph; the message says the plugin is not available for this gene. Does this mean you haven't drawn the graph or am I doing something wrong?

 

Any thoughts appreciated.

 

Many thanks

 

Kim

 

Dr Kim M Summers 
Division of Genetics and Genomics,
Roslin Institute and the Royal (Dick) School of Veterinary Studies
University of Edinburgh
Roslin Midlothian EH25 9PS Scotland, UK
tel: +44 (0) 131 527 4320
fax: +44 (0) 131 440 0434
e-mail: kim.s...@roslin.ed.ac.uk

Web: www.roslin.ed.ac.uk/kim-summers/

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[Andrew Su]

Hi Kim,

 

On Acta2, you've hit on an interesting case.  If you start at the Entrez Gene page for mouse Acta2 (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=retrieve&dopt=default&rn=1&list_uids=11475) and then click the HomoloGene link, you can see that Homologene associates mouse Acta2 with human ACTG2.  Currently, BioGPS displays the gene symbol for the "top-ranked" organism in the HomoloGene group (where the ranking goes human - mouse - rat - fly).  When you search BioGPS for "Acta2", you actually want to click on the entry for "ACTG2" and then switch the organism selector to "Mm", as shown in the screenshot below.  If anything isn't clear, please reply back and I will put together a quick screencast for you.  (And yes, we do have plans to make examples like these a bit more intuitive.)

 

 

 

Your second gene of interest is a bit more complex.  Let us investigate that one a bit further and we'll get back to you.

 

Cheers,

-andrew

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[Andrew Su]

Hi Kim,

 

Your second example of 2700049A03Rik is actually very similar to the first.  Here is the BioGPS search:

 

                http://biogps.gnf.org/?query=2700049A03Rik

 

As you can see, there are three results that are returned. 

 

The first record is shown as KIAA0586 and links to the Homologene record 8839 (human Entrez Gene 9786 and mouse Entrez Gene 76967).  "KIAA0586" is shown as the label because that is the official human gene symbol.  Clicking this link will show you the gene report for 9786 by default, and changing the species selector to mouse as described below will show you data for 76967.  After changing to mouse, you will see data for 1429595_at.

 

The second record is shown as "2700049A03Rik", which corresponds to the mouse Ensembl Gene ID ENSMUSG00000034601.  Unfortunately, Entrez Gene does not record a link between its entry 76967 and ENSMUSG00000034601, so this appears as a separate record.  1429595_at is a better match for 76967, so data for that probe set shows up under the first entry.

 

The third record is also shown as "2700049A03Rik", which this time corresponds to the rat Ensembl Gene ID ENSRNOG00000008244.  Again, in this case Entrez Gene does not store a cross reference to the Ensembl record, so this also appears as a separate record.

 

Hope that helps.  Please let us know if you have any other questions.

 

-andrew

 

 

 

From: Andrew Su
Sent: Tuesday, December 01, 2009 9:36 AM
To: 'kim summers (RI)'; 'bio...@googlegroups.com'
Subject: RE: Missing genes?

 

Hi Kim,

 

On Acta2, you've hit on an interesting case.  If you start at the Entrez Gene page for mouse Acta2 (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=retrieve&dopt=default&rn=1&list_uids=11475) and then click the HomoloGene link, you can see that Homologene associates mouse Acta2 with human ACTG2.  Currently, BioGPS displays the gene symbol for the "top-ranked" organism in the HomoloGene group (where the ranking goes human - mouse - rat - fly).  When you search BioGPS for "Acta2", you actually want to click on the entry for "ACTG2" and then switch the organism selector to "Mm", as shown in the screenshot below.  If anything isn't clear, please reply back and I will put together a quick screencast for you.  (And yes, we do have plans to make examples like these a bit more intuitive.)

 

 

 

Your second gene of interest is a bit more complex.  Let us investigate that one a bit further and we'll get back to you.

 

Cheers,

-andrew

 

 

From: kim summers (RI) [mailto:kim.s...@roslin.ed.ac.uk]
Sent: Tuesday, December 01, 2009 5:25 AM
To: 'bio...@googlegroups.com'
Subject: [BioGPS] Missing genes?

 

Dear BioGPS team

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