[Gramene] problematic GO term associations / Jaiswal-P et al., 2002

[Christine Oger]

Dear Gramene curation team,

I noticed some incongruities between GO terms 
associations in your database and in SP/Trembl 
(and RefSeq). I was using Blast2go and found 
weird GO term associations, namely histones 
associated with mitochondrion (GO:0005739)  and 
plastid (GO:0009536) (besides the expected 
nucleus and nucleosome). I tried to find where 
these mitochondria and plastids were coming from 
and It turned out the troublesome associations 
came from your database and were assigned 
manually,  backed up by the following reference :

Jaiswal-P, Lincoln-S, McCouch-S., "Subcellular 
localization of proteins listed in Gramene 
database", Gramene database, 2002, vol. 1, pp. 1-1

I guess it would be a good idea to have a look at 
all the accessions annotated during or using this 
work because many of them don't look right.

Below are a few of the examples I found of these 
troublesome GO term associations.

Thank you very much in advance for taking care of this.

Best regards,

Christine Oger




*********************
Q53NE3
*********************
in gramene:

mitochondrion (GO:0005739) 	Jaiswal-P et al., 2002 	 RCA
plastid (GO:0009536)	Jaiswal-P et al., 2002	RCA

in SP/TRembl:

GO:0000786;	Cellular component: nucleosome 
(inferred from electronic annotation from 
InterPro).
GO:0005634;	Cellular component: nucleus 
(inferred from electronic annotation from 
InterPro).
GO:0003677;	Molecular function: DNA binding 
(inferred from electronic annotation from 
InterPro).
GO:0006334;	Biological process: nucleosome 
assembly (inferred from electronic annotation 
from InterPro).

IPR009072; Histone-fold.
IPR007125; Histone_core_D.
IPR000164; Histone_H3.

**********
Q6L500
**********
in gramene

Molecular Function 	 DNA binding (GO:0003677) 	Jaiswal-P et al., 2003 
 
	IEA	With InterPro IPR007125
 
		With InterPro IPR007124
 
		With InterPro IPR002119
Biological Process	nucleosome assembly 
(GO:0006334)	Jaiswal-P et al., 2003
 
	IEA	 With InterPro IPR002119
  		chromosome organization and 
biogenesis (sensu Eukaryota) (GO:0007001) 
	Jaiswal-P et al., 2003
 
	IEA	 With InterPro IPR002119
Cellular Component	nucleus (GO:0005634)	Jaiswal-P et al., 2003
 
	IEA	 With InterPro IPR002119
	 	mitochondrion (GO:0005739)	Jaiswal-P et al., 2002	IEA
	 	nucleosome (GO:0000786)	Jaiswal-P et al., 2003
 
	IEA	 With InterPro IPR002119

in SP/TR
kw : Chromosomal protein; DNA-binding; Nucleosome core; Nucleus.
IPR009072; Histone-fold.	 (->GO:0003677 )
IPR007125; Histone_core_D.	(->GO:0003677 )
IPR002119; Histone_H2A.	 (-> Process	GO:0006334 nucleosome assembly
		               Function	GO:0003677 DNA binding
		               Component	GO:0000786 nucleosome
					GO:0005634 nucleus )

looking for other histones in gramenes I noticed 
the following accessions had also wrong GO term 
associations.
these erroneous terms are all associated with the Jaiswal-P et al., 2002  ref.
P08860  : plastid (GO:0009536)
Q9AXF0 plastid (GO:0009536)
Q8S857 mitochondrion
Q8LQJ1 plastid (GO:0009536)
Q8LLP5
Q8LHS7
...
and some more in the proteins associated with the 
Jaiswal-P et al., 2002 paper...


-- 
-----------------------------------
Dr Christine Oger
DTAMB / PRABI
Université Claude Bernard Lyon1
Bâtiment Gregor Mendel
43 blv du 11 nov 1918
F-69622 Villeurbanne
tel 33 (0)4 26 23 44 70
-----------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gramene/attachments/20080409/670acc40/attachment.html>