[Funcoup] GIN and DOM

[Andrey Alexeyenko]

> 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?
It's header is under
"***:  distinct genes/domains", i.e. I just counted how many unique 
genes occurred in the Pearson table.
This is also the reason that I do not know what to say about preparing 
the table and hence - cannot describe it in the Methods. I used just the 
Pearson linear correlation values in the standard form.

>
> 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?
That would be the hard part: how do we define a set of input genes?.. 
And I do not think it is crucial. Indeed, the pivotal dataset is 
UniDomInt: as soon as we have an extra gene with Pfam domains in it, we 
can check it in FunCoup with this data. For comparison, in MEX, PEX or 
PPI the gene IDs are pivotal, that's why we count them in the table.

> 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?
I think I just employed the old procedure developed for those old Rhodes 
data. And I ignored lines that had UniDomInt score 0.

A

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