Resource for the Analysis of
Signal Transduction in Cells
manually derived database of plant
sequence tags and genes up- or
down-regulated in response to various pathogens (biotic stress),
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
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
This gene expression database makes it possible to
the interaction between biotic and abiotic stress responses i.e.
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
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
includes information from a wide range
of plant species including Arabidopsis
), tomato (Lycopersicon
), potato (Solanum
etc. Database queries are a useful tool to assist in hypothesis
can then be tested through wet lab experimentation.
Have a look at the Help
to find out how best
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
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.
the following link to
access the database:-
Database Queries :
Fig 1. Venn diagram
showing interaction in Arabidopsis between salicylic acid, cold and
drought responses. Numbers refer to genes up- or down-regulated
Fig 2. Venn diagram showing interaction in Arabidopsis between
salicylic acid, phosphate starvation and sodium chloride. Numbers refer
to genes up- or down-regulated by treatment
Fig 3. Using the 'Roadmap' option to illustrate treatments in which the
phosphate induced gene phi1 (At4g08950) is either up- or down
regulated. This demonstrates just how many genes are regulated by
various treatments and that genes are not uniquely regulated by a
There are PDF diagrams in the Download section,
Arabidopsis signalling, ceramide signalling, cysteine metabolism,
glutamine / glutamate pathways, nuclear events associated with disease
resistance, phosphoinositide cascade, plant drought responses, ROS and
nitric oxide, SUMO and ubiquitin.
Potato Metabolic Pathways
DRASTIC gene expression database is
a manually curated database
which was originally set up in 2001 as a
collaborative project between staff at the Scottish Crop
and the University
of Abertay, Dundee.
A Powerpoint presentation on DRASTIC by Gary Lyon in 2004 is still
available and shows our thinking at that time, though some of the
facilities demonstrated in that talk are no longer available on this
to Powerpoint presentation).
Unfortunately, due to a combination of
events the DRASTIC web site was off-line
a number of years from November 2007 onwards, but in August 2012 it was
made available on line. The DRASTIC web site is currently being
managed by Gary Lyon in his retirement (Gary
INSIGHTS (INference of cell SIGnaling HypoTheseS) suite of web-based
tools allows intelligent data mining and extraction of information from
the DRASTIC database. Potential response pathways can be visualized and
comparisons made between gene expression patterns in response to
various treatments (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
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
Pathology 3: 103-9
which have referred to the
C. 2005. DRASTIC:
Biochemist August 2005, 47-48.
Shameer K, Ambika S, Varghese SM, Karaba N, Udayakumar M, Sowdhamini R.
2009. STIFDB - Arabidopsis stress responsive transcription factor
Journal of Genomics. Article ID 583429, 8 pages.
Sundar AS, Varghese SM, Shameer K, Karaba N, Udayakumar M, Sowdhamini
R. 2008. STIF: Identification of stress-upregulated transcription
factor binding sites in Arabidopsis
[Eds]. 2007. Induced
Resistance for Plant Defence. A Sustainable Approach to Crop Protection.
DRASTIC web site back on line 19 August
Contact : Gary Lyon (Email: firstname.lastname@example.org).
up-dated 8 June 2018.