[BioC] how to build a GOstats-compatible annotation package for plasmodium falciparum?
Marc Carlson
mcarlson at fhcrc.org
Tue Nov 6 18:27:45 CET 2007
Dave Berger wrote:
> Hi Paul
>
> we have developed a freely available tool and database for Plasmodium
> falciparum which amongst a range of other analyses, allows a user to
> search for over-represented GO terms in a cluster of co-expressed
> genes and provides a statistical test.
> perhaps it may be useful
> www.bi.up.ac.za/MADIBA/
>
> Philip Law - plaw at tuks.co.za - can be contacted for any queries
>
> best wishes
> Dave Berger
>
>
> Quoting Paul Shannon <pshannon at systemsbiology.org>:
>
>
>> I'm familiar with the YEAST data package, and the many chip-specific
>> annotation packages --
>> all of which work very nicely with GOstats.
>>
>> GO offers annotation for p.falciparum, the malaria parasite. What
>> would it take to
>> put that into an R data package which will work with GOstats?
>>
>> Thanks!
>>
>> - Paul
>>
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>>
I am pleased to see there is a lot of interest in p. falciparum because
it is without a doubt a nasty critter that has got to be dealt with.
Because there is enough interest that it should be possible to make
something worthwhile, I would like to add this to our pipeline as soon
as possible. But because of the recent massive overhaul to the way we
do annotations, this change can not be immediate. Since some of you are
obviously already doing A LOT to improve these annotations, I will of
course really appreciate any additional advice you could give me about
where to find the best possible information for this critter. But even
better would be if you could get your updated information into
repositories like NCBI since the world of critters I have to support is
already large (and growing). In the interim it might be most efficient
to use some of these services that have been suggested. In the longer
term, it sounds like it makes sense to provide solid annotation support
for this and so I will get to work on this asap.
Paul: If you need information like "gene to go term" mappings, I can
show you how to get that. But it seems that the standard sources from
the NCBI might not be as up to date as what they have at the Sanger so
you might want to look there 1st to see if you can get something more
current. When this project gets closer to completion, I will appreciate
it if someone was willing to be a guinea pig.
I would also be interested in hearing from you guys about what sorts of
information you would find to be the most immediately useful in an
annotation package for p. falciparum.
Marc
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