Introduction
A
manually derived database of
plant
expressed
sequence tags and genes up- or
down-regulated in response to various pathogens (biotic
stress),
chemical
treatments, and
abiotic stress such as
drought, salt and cold. The information in the
database is derived from over 630 refereed papers (e.g. from
Figures and Tables) and uniquely presents this information in a
user-friendly format. Gene names associated with certain
accession
numbers have
changed with time. Information on genes has been up-dated in
the database since the original publication dates so that some genes
originally described as 'unknown function' are now described using
current identities.
This gene expression database makes it possible to
gain an
insight
into
the interaction between biotic and abiotic stress responses i.e.
crosstalk. For
example, the Arabidopsis genes At2g14560 and At5g14920' are
down-regulated by cold and drought respectively but are
both up-regulated by BTH and by infection with an incompatible isolate
of
Peronospora
parasitica,
thus suggesting how resistance could be affected detrimentally by
environmental conditions. Further information is available on this web
site in the form of tables listing Arabidopsis genes which are
up-regulated by BTH or salicylic acid but down regulated by
cold (
LINK to
next page).
The database currently contains over 33,400
records and
includes information from a wide range
of plant species including
Arabidopsis
thaliana,
rice (
Oryza
sativa), tomato (
Lycopersicon
esculentum),
barley (
Hordeum
vulgare), potato (
Solanum
tuberosum)
etc. Database queries are a useful tool to assist in hypothesis
formation which
can then be tested through wet lab experimentation.
Have a look at the
Help
Files to find out how best
to
interrogate the database. Firstly, I suggest trying out the 'Roadmap'
option. Click on the link to the Gene Expression Database below, then
click on the link to 'Roadmap' on the left hand side. Highlight
At1g80840 (which is AtWRKY40) and click on 'submit' - it takes about 15
seconds for the server to present the results. The output
shows
all those treatments in which AtWRKY40 is upregulated in Arabidopsis,
and the numbers
refer to the number of genes which are upregulated by both
treatments. Click on a number to obtain a list of the genes. The 'Ref
ID' provides a link to the original publication.
Button
D, Heilbronn J, Ball L, Natanson
L, Gartland J, Gartland K,
Marshall B, Newton A, Lyon G. Drastic: A database resource for the
analysis of signal transduction in cells.
Poster
(PDF).
Lyon
GD, Newton AC, Marshall B. 2002.
The need for a standard gene
classification (a Nucleotide Function Code) and an automated data-based
tool to assist in understanding the molecular associations in cell
signalling in plant-pathogen interactions.
Molecular
Plant
Pathology 3: 103-9.
