[Funcoup] GIN and DOM

[Erik Sonnhammer]

Thanks!

GIN: I just realised that this data type is not described in the Methods 
section, which it should be as it is new.  Could you please provide a 
section? I'm surprised it's only 4880 interactions - above what cutoff 
was that?

DOM: I'm very unhappy with this just saying 3563 for all species - this 
is almost meaningless.  Are you saying that the mapping to genes was 
only done on the fly?  Could I perhaps ask Dimitri to try to extract the 
actual gene pairs numbers?
I also see that we don't describe the UniDomInt usage in the Methods 
section - do we need to?  Was some cutoff or other parameter used?

Also, could I please ask everybody to go through the paper looking for 
omissions, unclear parts, and other bugs.

/Erik

On 10/18/2011 12:33 PM, Andrey Alexeyenko wrote:
> http://funcoup.sbc.su.se/statistics_2.0.html fixed.
>
> BUT differently (see the page), as it was (close to) impossible to
> calculate the exact numbers:
>
> - in GIN: due to absence (at me) of the original pairwise file;
>
> - in DOM: because we store just the domain pairs, and answering exactly
> would take re0running the whole thing in the debug mode and looking at
> variable values...
>
> Andrey
>
> On 2011-09-28 12:02, Erik Sonnhammer wrote:
>> Great
>>
>> I guess you mean GIN. How about simply the nr of interactions (above the
>> cutoff whatever it was)?
>>
>> for DOM there should be a nr of interactions for each species while GIN
>> is only in yeast.
>>
>> /Erik
>>
>> On 09/28/2011 11:56 AM, Andrey Alexeyenko wrote:
>>> Hi,
>>>
>>> I updated statistics_2.0.html,
>>> except the columns DOM and INT where I do not know what to count.
>>>
>>> Andrey
>>>
>>> On 2011-09-27 11:42, Erik Sonnhammer wrote:
>>>> Here is a list:
>>>>
>>>> Put 2.0 on home page
>>>>
>>>> Update release notes (text file fine) with Input dataset sizes.
>>>>
>>>> On Erik's desktop (ubuntu), under Edge Catetories, Species, “fly”
>>>> becomes “...”
>>>>
>>>> Have KEGG pathway memberships and subcellular localisations been
>>>> updated?
>>>>
>>>> Why does not fly FBpp0289426 (NBS) align with its ortholog human NBN?
>>>>
>>>> Option to turn on debugging info
>>>>
>>>>
>>>> And some suggestions:
>>>>
>>>> Change to “(out of # at pfc>0.1):” under 'Network edges'. >0.25, >0.5,
>>>> 0.75 is a bit too course anyway and may not match the query.
>>>>
>>>> Update example queries(?)
>>>>
>>>> Add “maximum pfc” cutoff to the query – to look for novel links.
>>>>
>>>> Fewer areas on the webpage. Similar options should be grouped in one
>>>> area instead. A few areas with clear headers about what they contain is
>>>> preferable.
>>>>
>>>> /Erik
>>>>
>>>> On 09/27/2011 11:03 AM, Thomas Schmitt wrote:
>>>>> Awesome! What are the issues with the website that you want to get
>>>>> fixed?
>>>>> Is this something that we should do asap?
>>>>>
>>>>>
>>