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GO development

David Hill dph at informatics.jax.org
Tue Apr 24 10:43:20 PDT 2007


Julien,

This is a good question. In the past couple of weeks I was  making some 
gene sets for someone and have noticed something interesting with mouse 
genes as well. If I search for mouse genes that are associated with 
GO:0032502 'developmental process' there are 2846 genes. If I search for 
genes associated with GO:0007275 'multicellular organism development' 
there are 1963 genes. Clearly all mouse genes that function in a 
developmental process also function in multicellular organism 
development. When I examine this in have noticed that the discrepancy 
comes from two sources:

1) Annotations that are made to generic terms like 'cell death' and 
'cell differentiation'. In this case, we cannot link this term to the 
multicellular term because cell death or cell differentiation do not 
always happen in a multicellular organism. For the cases of cell 
differentiation, it is now our policy to use the cell type ontology to 
create GO terms that describe the differentiation of a cell type. Cell 
death is a bit more tricky because it is often tested in 'generic' cells 
in culture. We could create terms to describe cell death in every type 
of cell but I don't think that would be a practical approach.
2) An incompleteness of part_of relationships in the graph. In 
particular the differentiation of some cell types (fat cell  
differentiation ; GO:45444) that are only found in multicellular 
organisms are not part_of multicellular organism development. One of my 
plans is to clean these up, but when I do, I'd like to work in 
conjunction with the anatomy and cell type ontology groups since the 
precise placement in the graph would require a knowledge of which cell 
types are always found in which anatomical structures. I have cleaned 
some of these up when I am focusing on a certain area of the graph, but 
it is not as easy to place them in exactly the right place as it first 
seems.

I am planning to create a term called 'cell differentiation involved in 
multicellular organism development', make this term a part_of child of 
'multicellular organism development' and an is_a "cell differentiation" 
then place all the correct types of cell differentiation as is_a 
children of this term. It would solve part of the problem of not having 
gene products grouped correctly under 'multicellular organism 
development' but the part_of problem will still exist.

I also think that if a gene product from a multicellular organism is 
annotated to one of the more generic development terms, it should be 
co-annotated to 'multicellular organism development'. We would need to 
discuss what evidence code this would get. I suspect it would be IC.

For now, I would suggest that if you want all annotations for genes 
involved in the development of zebrafish, your should search for all 
genes that are annotated to 'developmental process' (GO:0032502) or its 
children.

David




 Julien Roux wrote:
> Hello everybody
>
> I was looking at the expression in zebrafish of developmental genes in 
> GO, annotated as (or under) multicellular organismal development, 
> <http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=GO:0007275&session_id=5369b1177431790>GO:0007275, 
> biological process.
> Surprisingly I find that compared to the rest of zebrafish genes, they 
> are less expressed at the beginning of development, expressed in 
> similar levels from segmentation stages to larval stages and then less 
> expressed in juvenile and adult.
> I would expect these genes to be overexpressed during the development 
> process...
> What do you think of that?
> What is classified as "development" in GO?
>
> Thanks for your help and ideas
> Julien
>



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