[Funcoup] Featured Article

[Erik Sonnhammer]

Hi,

The problem with "largest reconstruction of gene networks to date" is 
that STRING has 1000 species and is surely a lot larger (in total).

A way to clarify this would be:

The FunCoup 2.0 database provides the largest gene network 
reconstructions to date for 11 eukaryotes, ..."

But really to say this we should check if this is true for all 11 
species. Aside from STRING there are a bunch of other databases 
(referenced in our paper).  Any volunteers?

/Erik

On 11/29/2011 02:07 PM, Andrey Alexeyenko wrote:
> Hi,
>
> I suggest the most parsimonious (and least humble) edit:
> "provides the largest ROBUST reconstruction of gene networks to date,
> owing to the extensive transfer of evidence between species via
> orthologs AND SUPERVISED LEARNING ON SPECIES OWN DATA"
>
> This recognizes advantage compared to STRING. But if there is another
> database with more than ~50 million links in more that 10 eukaryotic
> species that uses orthologs and KEGG-based training sets, then it's
> wrong, and I'd agree with Erik's version.
>
> Andrey
>
> On 2011-11-29 13:31, Erik Sonnhammer wrote:
>> Hi, this is a nice surprise, see below.
>>
>> But personally I find their lay summary it a bit too boasting, given
>> that we only cover 11 species.
>>
>> how about
>>
>> The FunCoup 2.0 database provides very comprehensive reconstructions of
>> gene networks, owing to the extensive transfer of evidence between
>> species via orthologs, and Bayesian integration of nine different data
>> source types. The FunCoup website allows local network alignment between
>> multiple species.
>>
>> instead?
>>
>> /Erik
>>
>> -------- Original Message --------
>> Subject: Nucleic Acids Research - NAR-02446-DATA-E-2011.R1
>> Date: Tue, 29 Nov 2011 06:20:53 -0500 (EST)
>> From: nar at soton.ac.uk
>> To: erik.sonnhammer at sbc.su.se
>>
>> 29-Nov-2011
>>
>> NAR-02446-DATA-E-2011.R1 - Comparative interactomics with Funcoup 2.0
>>
>> Dear Prof. Sonnhammer:
>>
>> I am pleased to inform you that your article has been chosen by the
>> Editors of Nucleic Acids Research to appear on our Featured Articles
>> page
>> (http://www.oxfordjournals.org/our_journals/nar/featured_articles.html).
>> Featured Articles represent the top 5% of NAR papers in terms of
>> originality, significance and scientific excellence.
>>
>> Each article appearing on this page is accompanied by a short Lay
>> Summary. The Lay Summary for your article is added below for your
>> information. If you wish to make corrections to the Summary, please
>> email me within 48h of this email (nar at soton.ac.uk). Please note that
>> your Summary should be no longer than 100 words and only minor
>> corrections are allowed at this stage.
>>
>> Lay Summary:
>> The FunCoup 2.0 database provides the largest reconstruction of gene
>> networks to date, owing to the extensive transfer of evidence between
>> species via orthologs and Bayesian integration of nine different data
>> source types. The FunCoup website allows local network alignment between
>> multiple species.
>>
>> With best wishes
>>
>> Martine Bernardes Silva
>>
>> Nucleic Acids Research
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