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al., 2002</title></head><body>
<div><font face="Courier" size="-1" color="#000000"><br></font></div>
<div><font face="Arial">Dear Gramene curation team,</font></div>
<div><font face="Arial"><br></font></div>
<div><font face="Arial">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
:</font></div>
<div><font face="Arial"><br></font></div>
<div><font face="Arial">Jaiswal-P, Lincoln-S, McCouch-S.,
"Subcellular localization of proteins listed in Gramene
database", Gramene database, 2002, vol. 1, pp. 1-1</font></div>
<div><font face="Arial"><br></font></div>
<div><font face="Arial">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.</font></div>
<div><font face="Arial"><br></font></div>
<div><font face="Arial">Below are a few of the examples I found of
these troublesome GO term associations.</font></div>
<div><font face="Arial"><br></font></div>
<div><font face="Arial">Thank you very much in advance for taking care
of this.</font></div>
<div><font face="Arial"><br></font></div>
<div><font face="Arial">Best regards,</font></div>
<div><font face="Arial"><br></font></div>
<div><font face="Arial">Christine Oger</font></div>
<div><font face="Arial"><br></font></div>
<div><font face="Arial"><br></font></div>
<div><font face="Arial"><br></font></div>
<div><font face="Courier" size="-1" color="#000000"><br></font></div>
<div><font face="Courier" size="-1"
color="#000000">*********************</font></div>
<div><font face="Courier" size="-1"
color="#000000">Q53NE3</font></div>
<div><font face="Courier" size="-1"
color="#000000">*********************</font></div>
<div><font face="Courier" size="-1" color="#000000"><u>in
gramene:</u></font></div>
<div><font face="Courier" size="-1" color="#000000"><br></font></div>
<div><font face="Courier" size="-1" color="#000000">mitochondrion
(GO:0005739) <x-tab> </x-tab>Jaiswal-P et
al., 2002 <x-tab> </x-tab> RCA</font></div>
<div><font face="Courier" size="-1" color="#000000">plastid
(GO:0009536)<x-tab> </x-tab>Jaiswal-P et al.,
2002<x-tab> </x-tab>RCA</font></div>
<div><font face="Courier" size="-1"><br></font></div>
<div><font face="Courier" size="-1"><u>in SP/TRembl:</u></font></div>
<div><font face="Courier" size="-1"
color="#000000"><x-tab>
</x-tab></font></div>
<div><font face="Courier" size="-1"
color="#000000">GO:0000786;<x-tab>
</x-tab>Cellular component: nucleosome (inferred from electronic
annotation from InterPro).<br>
GO:0005634;<x-tab> </x-tab>Cellular component: nucleus (inferred
from electronic annotation from InterPro).<br>
GO:0003677;<x-tab> </x-tab>Molecular function:
DNA binding (inferred from electronic annotation from
InterPro).</font></div>
<div><font face="Courier" size="-1"
color="#000000">GO:0006334;<x-tab>
</x-tab>Biological process: nucleosome assembly (inferred from
electronic annotation from InterPro).</font></div>
<div><font face="Courier" size="-1" color="#000000"><br></font></div>
<div><font face="Courier" size="-1" color="#000000">IPR009072;
Histone-fold.</font></div>
<div><font face="Courier" size="-1" color="#000000">IPR007125;
Histone_core_D.<br>
IPR000164; Histone_H3.</font></div>
<div><font face="Courier" size="-1"><br></font></div>
<div><font face="Courier" size="-1">**********</font></div>
<div><font face="Courier" size="-1">Q6L500</font></div>
<div><font face="Courier" size="-1">**********</font></div>
<div><font face="Courier" size="-1"><u>in gramene</u></font></div>
<div><font face="Courier" size="-1"><br></font></div>
<div><font face="Courier" size="-1" color="#000000">Molecular
Function <x-tab> </x-tab> DNA binding
(GO:0003677) <x-tab>
</x-tab>Jaiswal-P et al., 2003 <x-tab> </x-tab></font></div>
<div><font face="Courier" size="-1"
color="#000000"><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab>IEA<x-tab> </x-tab>With InterPro
IPR007125</font></div>
<div><font face="Courier" size="-1"
color="#000000"><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab> </x-tab>With
InterPro IPR007124</font></div>
<div><font face="Courier" size="-1"
color="#000000"><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab> </x-tab>With
InterPro IPR002119</font></div>
<div><font face="Courier" size="-1" color="#000000">Biological
Process<x-tab> </x-tab>nucleosome
assembly (GO:0006334)<x-tab>
</x-tab>Jaiswal-P et al., 2003<x-tab> </x-tab><br>
<x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab>IEA<x-tab> </x-tab> With InterPro
IPR002119<br>
<x-tab>
</x-tab><x-tab>
</x-tab>chromosome organization and biogenesis (sensu Eukaryota)
(GO:0007001)<x-tab> </x-tab>Jaiswal-P et al., 2003<x-tab>
</x-tab><br>
<x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab>IEA<x-tab> </x-tab> With InterPro
IPR002119<br>
Cellular Component<x-tab>
</x-tab>nucleus (GO:0005634)<x-tab>
</x-tab>Jaiswal-P et al., 2003<x-tab> </x-tab><br>
<x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab>IEA<x-tab> </x-tab> With InterPro
IPR002119</font></div>
<div><font face="Courier" size="-1"
color="#000000"><x-tab>
</x-tab> <x-tab>
</x-tab>mitochondrion (GO:0005739)<x-tab>
</x-tab>Jaiswal-P et al., 2002<x-tab> </x-tab>IEA</font></div>
<div><font face="Courier" size="-1"
color="#000000"><x-tab>
</x-tab> <x-tab>
</x-tab>nucleosome (GO:0000786)<x-tab> </x-tab>Jaiswal-P et al.,
2003<x-tab> </x-tab></font></div>
<div><font face="Courier" size="-1"
color="#000000"><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab>IEA<x-tab> </x-tab> With InterPro
IPR002119</font></div>
<div><br></div>
<div><font face="Courier" size="-1"><u>in SP/TR</u></font></div>
<div><font face="Courier" size="-1">kw :<font color="#000000">
Chromosomal protein; DNA-binding; Nucleosome core;
Nucleus.</font></font></div>
<div><font face="Courier" size="-1" color="#000000">IPR009072;
Histone-fold.<x-tab>
</x-tab> (->GO:0003677 )</font></div>
<div><font face="Courier" size="-1" color="#000000">IPR007125;
Histone_core_D.<x-tab>
</x-tab>(->GO:0003677 )</font></div>
<div><font face="Courier" size="-1" color="#000000">IPR002119;
Histone_H2A.<x-tab> </x-tab> (</font><font face="Courier"
size="-1">-><font color="#000000"> Process<x-tab>
</x-tab>GO:0006334 nucleosome assembly</font></font></div>
<div><font face="Courier" size="-1"
color="#000000"><x-tab>
</x-tab><x-tab>
</x-tab
> <span
></span> Function<x-tab> </x-tab>GO:0003677 DNA
binding</font></div>
<div><font face="Courier" size="-1"
color="#000000"><x-tab>
</x-tab><x-tab>
</x-tab
> <span
></span>
Component<x-tab>
</x-tab>GO:0000786 nucleosome</font></div>
<div><font face="Courier" size="-1"
color="#000000"><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab>GO:0005634 nucleus</font><font face="Courier" size="-1">
)</font></div>
<div><br></div>
<div><font face="Courier" size="-1">looking for other histones in
gramenes I noticed the following accessions had also wrong GO term
associations.</font></div>
<div><font face="Courier" size="-1">these erroneous terms are all
associated with the<font color="#000000"> Jaiswal-P et al.,
2002 </font> ref.</font></div>
<div><font face="Courier" size="-1" color="#000000">P08860 :
plastid (GO:0009536)</font></div>
<div><font face="Courier" size="-1" color="#000000">Q9AXF0 plastid
(GO:0009536)</font></div>
<div><font face="Courier" size="-1"
color="#000000">Q8S857</font><font face="Courier" size="-1">
mitochondrion</font></div>
<div><font face="Courier" size="-1" color="#000000">Q8LQJ1 plastid
(GO:0009536)</font></div>
<div><font face="Courier" size="-1"
color="#000000">Q8LLP5</font></div>
<div><font face="Courier" size="-1"
color="#000000">Q8LHS7</font></div>
<div><font face="Courier" size="-1">...</font></div>
<div><font face="Courier" size="-1">and some more in the proteins
associated with the<font color="#000000"> Jaiswal-P et al.,
2002</font> paper</font>...</div>
<div><br></div>
<div><br></div>
<x-sigsep><pre>--
</pre></x-sigsep>
<div><font
color="#000000">-----------------------------------</font></div>
<div><font color="#000000">Dr Christine Oger<br>
DTAMB / PRABI<br>
Université Claude Bernard Lyon1<br>
Bâtiment Gregor Mendel<br>
43 blv du 11 nov 1918<br>
F-69622 Villeurbanne</font></div>
<div><font color="#000000">tel 33 (0)4 26 23 44 70</font></div>
<div><font
color="#000000">-----------------------------------</font></div>
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