[Funcoup] Featured Article

[Andrey Alexeyenko]

> The problem with "largest reconstruction of gene networks to date" is
> that STRING has 1000 species and is surely a lot larger (in total).
Hence I suggest "ROBUST  ... owing to ... orthologs AND SUPERVISED LEARNING"
> 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?
As soon as there is no DB with >10 species of comparable size, one can 
say "the largest reconstruction " - the latter term refers to the whole 
thing...

A

>
> /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
>>> _______________________________________________
>>> Funcoup mailing list
>>> Funcoup at sbc.su.se
>>> https://mail.sbc.su.se/mailman/listinfo/funcoup
>> _______________________________________________
>> Funcoup mailing list
>> Funcoup at sbc.su.se
>> https://mail.sbc.su.se/mailman/listinfo/funcoup
>
> _______________________________________________
> Funcoup mailing list
> Funcoup at sbc.su.se
> https://mail.sbc.su.se/mailman/listinfo/funcoup