expression database

pab6iah at LUCS-MAC.NOVELL.LEEDS.AC.UK pab6iah at LUCS-MAC.NOVELL.LEEDS.AC.UK
Tue Sep 27 07:08:39 EST 1994


Expression database.

    Garth Patterson posted a message enquiring about a database for 
C.elegans gene expression patterns. As many in the worm community 
know Andrew Lynch and David Briggs in my lab. are determining gene 
expression patterns for genes predicted in the genome sequence data. 
Promoter regions of  predicted genes are fused to a lacZ reporter and 
strains 
transformed with the fusion genes are examined. The results are being 
entered into ACEDB as searchable text items attached to the physical map / 
genome sequence items. Obviously this should be extended to include 
expression patterns determined by others. I was speaking with Richard 
Durbin a few months ago about this and and he did not feel he had the time 
to act as the collator of such entries. Richard suggested that perhaps I 
would 
have the time... Garth's message has stimulated me into action.
    Anyone who has a gene expression pattern which they would like entered 
into ACEDB may send such an entry to me. I will collect them together in to 
a format appropriate for rapid and easy entry into ACEDB and then pass 
them onto Richard. The text description should be a short paragraph in 
length. Bear in mind that such an entry is mainly for the benefit of others, 
so make sure that it is clear and could be readily identified in any text 
search 
that you foresee could be undertaken. There should also be a connection to 
data already in ACEDB, e.g a clone in the physical map or a gene predicted 
in the sequence data.
   Richard Durbin and I feel that text descriptions of expression patterns 
are 
of more value than images because they are readily searchable. However, 
images may be of value as they do contain additional information. Richard 
hasn't had the time to establish the capacity for such images within ACEDB, 
but Andrew Lynch has started putting images from my lab on the World 
Wide Web using the Hope Laboratory connection within the Caenorhabditis 
database set up by Leon Avery at Texas. This seems sufficient if we provide 
ways to relate between the two forms of presentation.
  I would value any comments on this.


Ian A. Hope.
Depts. Pure & Applied Biology / Genetics
Univ. of Leeds
England

i.a.hope at leeds.ac.uk



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