[Go] MT attachment to chromosome
Lisa Matthews
lmatthew at cshl.edu
Fri Nov 21 10:17:22 PST 2008
Hi Midori,
I know, it's good to be back in touch! I'm back in the USA now.
, I just had one question before popping the question over to Iain.
Based on the definition of Ndc80 complex and NMS Complex (and the fact
that Ndc80 associates with the kinetochore only during mitosis), I would
have thought that these terms would be "part of" condensed chromosome
kinetochore rather that the more generic kinetochore or am I missing
something(?)
* part_of relationship GO:0000776 : kinetochore [234 gene products]
<http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000776&session_id=7795amigo1227278122>
*
o close
<http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?action=minus_node&target=GO:0000777&term=GO:0000776&open_1=GO:0000777,GO:0000776&session_id=7795amigo1227278122#lineage>
is_a relationship GO:0000777 : condensed chromosome
kinetochore
<http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0000777&session_id=7795amigo1227278122>
[134 gene products]
<http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000777&session_id=7795amigo1227278122>
o
+ open
<http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?action=plus_node&target=GO:0000778&term=GO:0000776&open_1=GO:0000777,GO:0000776&session_id=7795amigo1227278122#lineage>
is_a relationship GO:0000778 : condensed nuclear
chromosome kinetochore
<http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0000778&session_id=7795amigo1227278122>
[69 gene products]
<http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000778&session_id=7795amigo1227278122>
+ open
<http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?action=plus_node&target=GO:0000939&term=GO:0000776&open_1=GO:0000777,GO:0000776&session_id=7795amigo1227278122#lineage>
part_of relationship GO:0000939 : inner kinetochore of
condensed chromosome
<http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0000939&session_id=7795amigo1227278122>
[34 gene products]
<http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000939&session_id=7795amigo1227278122>
+ open
<http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?action=plus_node&target=GO:0000444&term=GO:0000776&open_1=GO:0000777,GO:0000776&session_id=7795amigo1227278122#lineage>
part_of relationship GO:0000444 : MIS12/MIND type
complex
<http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0000444&session_id=7795amigo1227278122>
[18 gene products]
<http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000444&session_id=7795amigo1227278122>
+ leaf node part_of relationship GO:0033551 : monopolin
complex
<http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0033551&session_id=7795amigo1227278122>
[8 gene products]
<http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0033551&session_id=7795amigo1227278122>
+ open
<http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?action=plus_node&target=GO:0000940&term=GO:0000776&open_1=GO:0000777,GO:0000776&session_id=7795amigo1227278122#lineage>
part_of relationship GO:0000940 : outer kinetochore of
condensed chromosome
<http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0000940&session_id=7795amigo1227278122>
[17 gene products]
<http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000940&session_id=7795amigo1227278122>
o leaf node part_of relationship GO:0031262 : Ndc80 complex
<http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0031262&session_id=7795amigo1227278122>
[16 gene products]
<http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0031262&session_id=7795amigo1227278122>
o leaf node part_of relationship GO:0031617 : NMS complex
<http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0031617&session_id=7795amigo1227278122>
[13 gene products]
<http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0031617&session_id=7795amigo1227278122>
:
Ndc80 Complex
A supercomplex formed by the association of two subcomplexes (known as
MIND and Ndc80 in Schizosaccharomyces) with additional proteins at the
kinetochores of condensed nuclear chromosomes. [source: PMID:16079914
<http://www.ncbi.nlm.nih.gov/pubmed/16079914>]
NMS Complex:
A supercomplex formed by the association of two subcomplexes (known
as MIND and Ndc80 in Schizosaccharomyces) with additional proteins
at the kinetochores of condensed nuclear chromosomes. [source:
PMID:16079914 <http://www.ncbi.nlm.nih.gov/pubmed/16079914>]
Thanks,
Lisa
Midori Harris wrote:
> Hi Lisa,
>
> It would be great if you could ask Iain Cheeseman what he thinks. We
> seem to be converging on agreeing that kinetochore-port_of-chromosome
> is the best we can do for now, until we implement more relationship
> types, but it can't hurt to get an expert's view.
>
> (Great to hear fraom you again, too -- it's been a while!)
>
> Midori
>
> On Fri, 21 Nov 2008, Lisa Matthews wrote:
>
>> Hi all,
>> There is a really good review that just came out on this written by
>> the Cheeseman group (they've done a lot on defining the highly
>> conserved kinetochore DNA to microtubule molecular connectivity
>> PMID: 19000831. I can run this question by Iain Cheeseman who has
>> recently helped Reactome out with some annotations on centrosome
>> function.
>> Lisa
>>
>> Valerie Wood wrote:
>>> Currently a placement of kinetochore under chromosome would be correct
>>> based on how condensed nuclear centromeric region is defined
>>>
>>> def
>>> condensed nuclear chromosome, centromeric region
>>> The region of a condensed chromosome in the nucleus that includes
>>> the centromere and associated proteins, including the kinetochore.
>>> In monocentric chromosomes, this region corresponds to a single area
>>> of the chromosome, whereas in holocentric chromosomes, it is evenly
>>> distributed along the chromosome.
>>>
>>> which is a child of chromosome
>>> although at present kinetochore is not a child of this term
>>>
>>> I don't know what is right though.
>>>
>>> VAl
>>>
>>> Midori Harris <midori at ebi.ac.uk> wrote:
>>>> I think what would really help are those spatial relationship types
>>>> that we've talked about with Chris. Kinetochore-chromosome is one
>>>> of many cases where I suspect that biologists would expect to see
>>>> some connection (tho I'm sure Rex or Val can correct me if I'm
>>>> wrong), so we've used part_of even though it's far from ideal.
>>>>
>>>> m
>>>>
>>>> On Fri, 21 Nov 2008, David Hill wrote:
>>>>
>>>>
>>>>> I'm not sure the kinetochore should be a part_of the chromosome.
>>>>> It attaches to the centromere, which is part of the chromosome. I
>>>>> think we might want to have Rex weigh in on this too. He's a cell
>>>>> biologist.
>>>>>
>>>>> David
>>>>>
>>>>> Midori Harris wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Working on some cross-product definitions, I came up with a
>>>>>> question about whether two terms that are currently siblings
>>>>>> should have an is_a link. The terms are:
>>>>>>
>>>>>> attachment of spindle microtubules to chromosome GO:0051313
>>>>>> attachment of spindle microtubules to kinetochore GO:0008608
>>>>>>
>>>>>> and I think we shoud have GO:0008608 is_a GO:0051313 because
>>>>>> kinetochore is part_of chromosome in the component ontology.
>>>>>>
>>>>>> I've opened a SourceForge item, and I'd appreciate any comments.
>>>>>>
>>>>>> https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2320413&group_id=36855
>>>>>> thanks,
>>>>>> midori
>>>>>>
>>>>>> _______________________________________________
>>>>>> Go mailing list
>>>>>> Go at geneontology.org
>>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>>
>>>>>
>>>> _______________________________________________
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>>>>
>>>>
>>>>
>>>
>>>
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