[Gramene] total number of oryza sativa genes [shuly, liya, chengzhi]

[Pankaj Jaiswal]

There are a couple of queries, that may involve querying proteindb and 
the ensembl:

How many proteindb entries from
	#1 species = Oryza sativa
Have GO annotations
	#2 Total no of associations
	#3 Unique no of proteins with associations
How many have non-IEA annotations
	#4 Total no of non-IEA associations
	#5 Unique no of proteins with non-IEA associations
Of these (#5) how many map to the TIGR LOCUS ID (e.g. LOC_Osxxgxxxxx)

This will tell how many TIGR loci have proteins mapped to it that have 
non-IEA annotations (total and unique).

Also give me how many unique genedb entries from Oryza sativa have GO 
annotations (unique and total associations). And of these how many map 
to the TIGR_locus_ID>

Pankaj

Sue Rhee wrote:
> Hi Liya,
> 
> I have read the readme file before sending out this request. I am 
> interested only in Oryza sativa numbers (see below my original email) 
> and I do not see that in the GO readme file. I see the numbers in NCBI's 
> taxon db, but their numbers are somewhat strange and I would prefer to 
> get them from your database, if you have them.
> 
> Thanks
> Sue
> 
> Liya Ren wrote:
>> Hi Sue,
>>
>> I have put the statistics in gramene_oryza.README file in GO database. 
>> The attachment is the statistics part.
>>
>> Liya
>>
>>
>>
>> On Nov 18, 2007, at 1:45 AM, sue rhee wrote:
>>
>>> Hi: I'm trying to get the portion of GO annotated O. sativa (sativa, 
>>> sativa-japonica, sativa-indica) genes and I got the numbers of 
>>> annotated genes from the GO database (see below) but couldn't get the 
>>> number of genes in this species. Please help.
>>>
>>> species    experimental annotations    total annotations    portion 
>>> expt annotations    annotated gene products    total gene products 
>>> portion annotated
>>> rice    403    85312    0.5%    63876
>>>
>>> Thanks,
>>> Sue
>>>
>>> ----------------------------------------------------------------------------- 
>>>
>>> Sue Rhee                             rhee at acoma.stanford.edu
>>> The Arabidopsis Information Resource    URL: www.arabidopsis.org
>>> Carnegie Institution of Washington    FAX: +1-650-325-6857
>>> Department of Plant Biology        Tel: +1-650-325-1521 ext. 251
>>> 260 Panama St.
>>> Stanford, CA 94305
>>> U.S.A.
>>> ----------------------------------------------------------------------------- 
>>>
>>> _______________________________________________
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>>
> 

-- 
Pankaj Jaiswal
G-15, Bradfield Hall
Dept. of Plant Breeding and Genetics
Cornell University
Ithaca, NY-14853, USA

Ph. +1-607-255-3103 / 4199
fax: +1-607-255-6683