[Go] [go] annotations for refgenomes

[David Hill]

Hi Sue and Mike,

I think including/separating out the annotations to the root nodes would 
be informative as well.

David

Sue Rhee wrote:
> Great. Actually, it would be very interesting to include the unknowns 
> in the graph. Since you color-code by the evidence codes, the NDs 
> would be a separate color, no? I think knowing the extent of the 
> unknown is quite useful..
>
> I would love to see last year's graph. I think these graphs would be 
> very cool to have on the GO website at some point, given that the 
> participating groups are OK with that.
>
> Cheers,
> Sue
>
> Mike Cherry wrote:
>> Sue,
>>
>> Thanks I'm glad you like the graph.  I have the graph from last year  
>> if anyone wants it.
>>
>> Good question about the filtering.  The filtering different between  
>> the two graphs simply refers to the nightly filtering of gene  
>> association files.  This includes a large list of potential "errors"  
>> that are removed including badly formated information, syntax 
>> errors,  use of obsolete GOIDs.  The normal filtering.  Thats good 
>> that there  isn't much different between the two graphs.
>>
>> For both graphs I remove all the annotations to the roots: 
>> GO:0008150,  GO:0003674, GO:0005575.  Then count the number of IDs in 
>> column 2.   For TAIR there are 20,500 unique IDs for Function 
>> annotations with the  root annotations excluded.
>>
>> -Mike
>>
>>
>> On Feb 27, 2008, at 6:25 PM, Sue Rhee wrote:
>>
>>  
>>> Hi Mike,
>>>
>>> It's a beautiful graph. Thanks for sharing. I have a couple of  
>>> questions though. What is being filtered out? It seems to me the 
>>> two  graphs are very similar. Also I'm a little confused about the 
>>> total  number of genes. In TAIR, we have 24465 (for function), 23534 
>>> (for  process), and 22038 (for component) protein-encoding genes 
>>> annotated  with GO, but the graphs seem to be showing different 
>>> numbers.
>>>
>>> Sue
>>>
>>> Mike Cherry wrote:
>>>    
>>>> Graphs I made list week.  One is from the submitted GA file and 
>>>> one  from the filtered GA file.
>>>>
>>>> -Mike
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>       
>>> -- 
>>> Sue Rhee
>>> Staff Scientist
>>> Carnegie Institution, Department of Plant Biology
>>> 260 Panama Street, Stanford, CA 94305
>>> Email: (650) 325-1521 x251
>>> Fax: (650) 325-6857
>>>     
>>
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