[Go] [go] annotations for refgenomes

[Sue Rhee]

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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-- 
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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