[annotation] Re: GO Help query on microRNAs (fwd)

[Amelia Ireland]

Hi annotators,

This query came from GO help - does anyone know how many mammalian
microRNAs have (biological process) annotations??

> Does this mean that there are very few mammalian microRNAs with
> Biological Process annotation?  Do you happen to have numbers on that?

Thanks,
Amelia.

-- 
Amelia Ireland
GO Editorial Office,
European Bioinformatics Institute, UK.
Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp

---------- Forwarded message ----------
Date: Mon, 8 Oct 2007 19:58:47 -0400 (EDT)
From: mlbulyk at receptor.med.harvard.edu
To: aji at ebi.ac.uk
Subject: Re: GO Help query on microRNAs (fwd)

Thank you for your reply, Amelia (& Ceri).

Does this mean that there are very few mammalian microRNAs with Biological
Process annotation?  Do you happen to have numbers on that?

Thank you very much,
Martha

-- 
Martha Bulyk
Assistant Professor of Medicine, Pathology, and Health Sciences &
Technology (HST)
Brigham & Women's Hospital and Harvard Medical School


> Dear Martha,
>
> In answer to your question about mammalian microRNA annotation, one of
> the ZFIN [zebrafish] annotation team responded as follows:
>
>
> I have done most of the curation for zebrafish microRNA genes (mirn)
> at ZFIN.   We endeavor to capture GO from the literature for all
> genes including the microRNA genes.
>
> There are 4 GO terms that can be specifically associated with the
> mirn genes themselves, miRNA-mediated gene silencing (GO:0035195) and
> micro-ribonucleoprotein complex (GO:0035068), miRNA-mediated gene
> silencing, negative regulation of translation (GO:0035278) and
> miRNA-mediated gene silencing, mRNA cleavage (GO:0035279).    There
> are other functions that can be curated but they are not exclusively
> microRNA  functions and tend to be biological processes.
> We have 68 microRNA genes annotated with miRNA-mediated gene
> silencing (GO:0035195).
>
> Most authors working with zebrafish seem only to state that a
> particular sequence is a microRNA and so it must be involved in
> miRNA-mediated gene silencing (GO:0035195).  This means most of our
> annotations have the evidence code NAS.  There are a few instances of
> authors saying this zebrafish microRNA is like that mouse microRNA
> but the mouse microRNA does not have any GO so we can't really use
> the ISS evidence code and comply with the reference genome guidelines.
>
> Hope this helps,
> Ceri Van Slyke
> ZFIN
>
> --
>
> I hope that this response is of use to you. If you have any further
> questions, please do not hesitate to contact the GO helpdesk again.
>
> Kind regards,
> Amelia Ireland.
>
> --
> Amelia Ireland, GO Helpdesk
> GO Editorial Office,
> European Bioinformatics Institute, UK.
> Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp
>
>
>