[Go] [go] annotations for refgenomes

[Mike Cherry]

Sue,

A graph with annotations to the root and ND annotations can be found at:

   http://genetics.stanford.edu/~cherry/RefGenome-with-ND.pdf

I put it there to reduce the size of this email.

-Mike

On Feb 27, 2008, at 10:32 PM, 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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>
> -- 
> 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