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how to define GO groups with a certain size boundary

Ana Conesa aconesa at ivia.es
Wed Nov 9 15:16:08 PST 2005


Dear Albert,

You might like to have a look our tool Blast2GO for addressing the issues 
you are posting. Blast2GO is a GO tool for GO annotation of non-annotated 
sequences, which also includes a number of functions for GO analysis. It 
accepts an already existing annotation file, so you can use only the GO 
analysis part of the tool.
In particular, we have just included a new feature to map an existing 
annotation to a GOSlim annotation. We currently support the GOSlim´s 
available at the GO Consortium site, but it would not be difficult to add a 
new GOSlim database if you creat your own one.
Additionally the application generates Combined Graphs for a set of 
annotated genes. When doing so you can modulate the size and form of the 
resulting DAG by selecting a filter on the counts at each node. We provided 
2 ways to do this, but the simplest one would cut your tree at nodes having 
at least a given number of genes. So, you will visualize a DAG that for some 
branches will be deeper than for others and the end of the branches will 
have nodes with the same number of annotated sequences. This graph 
information can be also viewed as a multilevel pie: this is a pie chart 
representation of the projection of the DAG to the lowest level of each 
branch that contains a specified number of sequences.

If you think these functionalities could help you in your analysis, you can 
download our tool from www.blast2go.de. Do not hesitate to contact us for 
any question or comments

Best regards,

Ana Conesa


On Tue, 08 Nov 2005 15:55:37 +0100, Albert Vilella wrote
> Hi all go-dev-elopers and gofriends,
> 
> > >> I am trying to split a large subset of the GO-annotated Flybase
> genes
> > >> into GO groups to use them as categories for my analyses.
> > >> 
> > >> But I would like to try and merge the groups that have too few
> genes
> > >> into their upper GO level and split those that accumulate too
> > >> much genes into their lower GO level.
> > >> 
> > >> For what I have seen in most of the published articles, this is
> just
> > >> the other way around of what most people (for example, in the
> > >> microarrays field) is doing: performing an analysis to obtain a
> subset
> > >> of genes, then look for enrichments in the GO DB distribution of
> > >> ids.
> > >> 
> > >> I would like to ask if anybody has stumbled over this situation
> before
> > >> or if anyone has any suggestion about how to do this.
> > >> 
> > >> It is worth to mention that this merge/split trick was used in the
> > >> paper of the chimp genome ("Initial sequence of the chimpanzee
> genome
> > >> and comparison with the human genome" (Nature)) although they did
> it
> > >> "a posteriori" only in the categories that showed a significant
> > >> diference to a given analysis.
> 
> El dt 08 de 11 del 2005 a les 13:45 +0000, en/na Jane Lomax va escriure:
> 
> > Hi Albert - as far as know there isn't an easy way to do this, but
> I'll 
> > explain the long way to do it. It may be worth emailing GO friends 
> > (gofriends at geneontology.org) though, as there are often tools out
> there 
> > that we don't yet know about.
> > 
> > So a way you could do it would be to create your own set of high-level
> GO 
> > categories (called a GO slim, see 
> > http://www.geneontology.org/GO.slims.shtml), and then use this to sort
> out 
> > your annotation set into those categories. You can create a GO slim
> using 
> > DAG-Edit (http://www.geneontology.org/GO.tools.shtml#in_house) - there
> are 
> > some instructions on doing this here: 
> > 
> > http://www.geneontology.org/GO.teaching.resources.shtml#tut
> > 
> > (I will get round to making proper documentation for doing this soon,
> I 
> > promise!). Then you can use the Perl script map2slim 
> > (http://www.geneontology.org/GO.slims.shtml#script) to 'bucket' your 
> > annotations into your categories - it may be easier for you to use a 
> > web-based implementation of this script e.g. Generic GO Term Mapper
> > (http://www.geneontology.org/GO.tools.other.shtml#ggtm).
> > 
> > The difficult thing will be that you will have to keep adjusting your 
> > GO slim set and re-running the mapping script to see which categories
> have 
> > too many annotations until you get the correct balance. It would be
> nice 
> > to have a tool to do this automatically.
> 
> Yes, from my humble biological-degree-not-graph-theory-guru
> background, I understand that the tricky bit of this stuff is to
> balance the categories: split the large GOids into their childs and
> merge the small GOids into their parent.
> 
> For the tiny amount of investigation I made, I believe that if GO 
> were a cyclic graph, this would be a challenging algorithm.
> 
> But with a DAG with the characteristics of GO, I bet there must be a
> graph theory guru that can enlighten me on this issue with an
> algorithm that does this adjustments.
> 
> Manually balancing the DAG is worth the try.
> 
> Anyone any hint?
> 
> Bests,
> 
>     Albert.
> 
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