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help about total number of genes within various genomes

Michelle Giglio (Gwinn) mlgwinn at tigr.org
Fri Mar 12 12:21:02 PST 2004


Hi Linda,

I know you are getting the TIGR genome totals from the CMR, but here is 
a summary of TIGR's prokaryotic totals and an explanation of the genes 
without GO terms.

organism              total genes             total genes with GO
V. cholera              3885                        2925
B. anthracis           5507                        4417
S. oneidensis         4930                        3696
C. brunetii              2135                        1366
P. syringae             5763                        3137
G. sulfurreducens  3533                        2803

In all cases but P. syringae, most of the genes not annotated to GO are 
proteins that have been named "hypothetical protein".  These proteins 
have no homology to any other protein or motif and are not known to be 
expressed.  A long time back, the GO made the decision that purely 
hypothetical proteins should not get GO terms.  There are some proteins 
from each genome that are not hypothetical and which don't have GO terms 
and most of these have fairly serious reading frame disruptions and are 
not considered to be expressed.

The exception to what I said above is P. syrinage - this one was 
annotated during a time when we could not devote full time to GO 
annotation and therefore does not have all of its genes annotated.  
There is an effort underway by another group (the Pseudomonas community 
annotation project) to complete the GO terms for P. syringae.

Let me know if you need any other information.

Michelle



>
>On Fri, 12 Mar 2004, linda mcmahan wrote:
>
>  
>
>>Hi GO friends,
>>
>>Could you please advise me on the best web resources where I can get
>>the approximate total number of genes (GO annotated genes + GO
>>unannotated genes) within the organisms of those genomes that have gene
>>association files at  ftp://ftp.geneontology.org/go/gene-associations/.
>>   Thanks.
>>
>>Linda
>>
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>>    
>>
>
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