[Go] [go] annotations for refgenomes

[Sue Rhee]

Yay! It's awesome. I agree with Val that it would be nice to see the ND 
annotations to the root on top. This will show pretty clearly how much 
is known to be known and not known in each organism.

Sue

Mike Cherry wrote:
> 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

-- 
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