DRASTIC--INSIGHTS: querying information in a plant gene expression database

Abstract

DRASTIC--Database Resource for the Analysis of Signal Transduction In Cells (http://www.drastic.org.uk/) has been created as a first step towards a data-based approach for constructing signal transduction pathways. DRASTIC is a relational database of plant expressed sequence tags and genes up- or down-regulated in response to various pathogens, chemical exposure or other treatments such as drought, salt and low temperature. More than 17700 records have been obtained from 306 treatments affecting 73 plant species from 512 peer-reviewed publications with most emphasis being placed on data from Arabidopsis thaliana. DRASTIC has been developed by the Scottish Crop Research Institute and the University of Abertay Dundee and allows rapid identification of plant genes that are up- or down-regulated by multiple treatments and those that are regulated by a very limited (or perhaps a single) treatment. 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. The knowledge gained informs plant signalling pathways and systems biology investigations.

Figure 1

Web interface for the Pathway tool. (A) The search page for a set of AGI numbers. The pathway result is shown in (B). Up-regulated genes are shown in red. Down-regulated genes are shown in blue. Green cells indicate that both up- and down-regulation record(s) are held in DRASTIC. The pathway can be further mined by choosing any coloured cell which will display all the records for the AGI/treatment combination as shown in (C). The references for each record can be selected as shown in (D).

Figure 2

Web interface for the Roadmap tool. In this example, treatments up-regulating At3g45640 (MAP Kinase 3) were selected for investigation. (A) The resulting roadmap. From the DRASTIC data, 12 treatments up-regulate Atg45640. Using these treatments as the ‘lookup co-ordinates’, the map displays the total number of unique AGIs up-regulated by these treatments. The shaded squares hold the total number of genes up-regulated by a single treatment, and the numbers in the unshaded squares show the number of genes co-regulated by treatments. This map can be further mined by clicking on any of the squares to display the supporting records (see (B) where the co-ordinates wound and UV have been selected). Each record has a link to the reference it was curated from as shown in (C).