DRASTIC

DRASTIC logo

Database Resource for the Analysis of Signal Transduction in Cells

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.

 

        Database Access

         Click the following link to access the database:-
Gene Expression Database Statistics and Tools for searching the Database  (Database updated  12 June 2016) (Error messages: if you get a '505' error message try repeating the request in a different web browser eg Internet Explorer)
 
        Help Files
       

        Results from Database Queries :

Elicitor / Environment Interactions  1. Arabidopsis genes upregulated by BTH or salicylic acid and down regulated by cold
2. Arabidopsis genes upregulated by BTH and down regulated by drought (updated 9 July 2014)
3. Arabidopsis genes upregulated by BTH or salicylic acid and down regulated by phosphate starvation
4. Arabidopsis genes upregulated by BTH or salicylic acid and down regulated by sodium chloride
Arabidopsis sucrose nonfermenting (Snf1)-related kinases (SnRKs)
Arabidopsis calreticulin gene expression
Arabidopsis - common pathways for ABA, cold, drought, and sodium chloride
Arabidopsis - Botrytis cinerea and salicylic acid highlighting different responses of some genes
           

Fig 1. Venn diagram showing interaction in Arabidopsis between salicylic acid, cold and drought responses. Numbers refer to genes up- or down-regulated by treatment.


Venn diagram SA / cold / drought interaction

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

Venn diagram SA / phosphate starvation / sodium chloride interaction


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 single treatment.
Roadmap for phosphate-induced phi1 gene

           

            Links 
                 Links to other Databases on Plant Science

                There are PDF diagrams in the Download section, including:- 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
                 Gary Lyon Biography

                LINK to PDF Diagram of Metabolic Pathways of the Diseased Potato (Also available at www.potatometabolicpathways.webs.com)


              Potato Metabolic Pathways
Metabolic Pathways of the Diseased Potato

History of DRASTIC

The 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 Research Institute (SCRI) 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 site (LINK to Powerpoint presentation). Unfortunately, due to a combination of  events the DRASTIC web site was off-line for a number of years from November 2007 onwards, but in August 2012 it was again made available on line. The DRASTIC web site is currently being managed by Gary Lyon in his retirement (Gary Lyon Biography).

The 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 et al., 2006).

Publications

Button DK, Gartland KMA, Ball LD, Natanson L, Gartland JS, Lyon GD. 2006. DRASTIC-INSIGHTS: querying information in a plant gene expression database. Nucleic Acids Research 34 (Database issue): D712-D716.

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.

Lyon, GD, Newton AC, Marshall B, Ball L, Houston A, Natanson L.  Drastic: A database resource for the analysis of signal transduction in cells. Poster PDF.
 
Newton A, Lyon G, Marshall B. 2002. DRASTIC: a Database Resource for Analysis of Signal Transduction in Cells. BSPP News Summer 2002 - Online Edition., Number 42.


Other publications which have referred to the DRASTIC database

Canevet C. 2008. ONDEX visualization toolkit (OVTK) user tutorial. (see section 5.1).

Lyon GD. 2011. Diagrams on plant metabolic pathways including drought pathways.  http://potatometabolicpathways.webs.com/drought.htm

Ma C, Xin M, Feldmann KA, Wang X. 2014. Machine learning-based differential network analysis: a study of stress-responsive transcriptomes in Arabidopsis. Plant Cell 26, 520-37.

Moscatiello R, Mariani P, Sanders D, Maathius FJM. 2006. Transcriptional analysis of calcium-dependent and calcium-independent signalling pathways induced by oligogalacturonides. Journal of Experimental Botany 57, 2847-65.

Sansom C. 2005. DRASTIC: www.drastic.org.uk. The Biochemist August 2005, 47-48.
 
Shameer K, Ambika S, Varghese SM, Karaba N, Udayakumar M, Sowdhamini R. 2009. STIFDB - Arabidopsis stress responsive transcription factor database. International 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 thaliana. Bioinformation 2, 431-437.


Walters D, Newton A, Lyon G [Eds]. 2007. Induced Resistance for Plant Defence. A Sustainable Approach to Crop Protection. Blackwell Publishing.


DRASTIC web site back on line 19 August 2012

Contact : Gary Lyon (Email: garydavidlyon@gmail.com).      Web site last up-dated 12 June 2016