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

[Pankaj Jaiswal]

Dear Christine,

We are looking into the problem. Thanks for reporting it.

Pankaj

Christine Oger wrote:
> 
> 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
> -----------------------------------
> 
> 
> ------------------------------------------------------------------------
> 
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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