AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors

Abstract

Background: The gene regulatory information is hardwired in the promoter regions formed by cis-regulatory elements that bind specific transcription factors (TFs). Hence, establishing the architecture of plant promoters is fundamental to understanding gene expression. The determination of the regulatory circuits controlled by each TF and the identification of the cis-regulatory sequences for all genes have been identified as two of the goals of the Multinational Coordinated Arabidopsis thaliana Functional Genomics Project by the Multinational Arabidopsis Steering Committee (June 2002).

Results: AGRIS is an information resource of Arabidopsis promoter sequences, transcription factors and their target genes. AGRIS currently contains two databases, AtTFDB (Arabidopsis thaliana transcription factor database) and AtcisDB (Arabidopsis thaliana cis-regulatory database). AtTFDB contains information on approximately 1,400 transcription factors identified through motif searches and grouped into 34 families. AtTFDB links the sequence of the transcription factors with available mutants and, when known, with the possible genes they may regulate. AtcisDB consists of the 5' regulatory sequences of all 29,388 annotated genes with a description of the corresponding cis-regulatory elements. Users can search the databases for (i) promoter sequences, (ii) a transcription factor, (iii) a direct target genes for a specific transcription factor, or (vi) a regulatory network that consists of transcription factors and their target genes.

Conclusion: AGRIS provides the necessary software tools on Arabidopsis transcription factors and their putative binding sites on all genes to initiate the identification of transcriptional regulatory networks in the model dicotyledoneous plant Arabidopsis thaliana. AGRIS can be accessed from http://arabidopsis.med.ohio-state.edu.

Figure 1

Data flow of AtcisDB The rectangular boxes with right shadow represents the data sources, the rectangular boxes with left shadow represent the final data tables, arrows represent the direction of data flow, eclipses represent computational operations implemented in data-mining pipeline.

Figure 2

Database schema of AtcisDB Schematics diagram illustrating the interrelationship between the tables of the AtcisDB. The * represents the primary key and line with arrow link the foreign keys that associate each relational table.

Figure 3

Database schema of AtTFDB Schematics diagram illustrating the interrelationship between the tables of the AtTFDB. This first step was the most time intensive and accounted for approximately 75% of the total development time.

Figure 4

AGRIS system diagram A simplified diagram representing the interaction of different components of AGRIS.

Figure 5

Web page for searching AtcisDB Users can use a gene name or gene symbol to search the promoter of a specific gene and a set of genes regulated by a specific transcription factor.

Figure 6

A screen shot of an Arabidopsis gene promoter with annotation of cis-regulatory elements Users can use a gene name or gene symbol to search the promoter of a specific gene and a set of genes regulated by a specific transcription factor. The graphical interface was developed using GDVTK. The position of translation start site (ATG) is indicated by a line with small arrow. The region upstream of ATG is considered as the promoter region of the corresponding gene. A set of small colored boxes represent the transcription factor binding sites. The boxes that are above the line represent the sites on positive strand and those that are below the line represent sites on negative strand. When the user moves the mouse on the colored squares, a contextual menu pops up to show the detailed information for that binding site. The sequence of the promoter can be obtained by clicking the link on Get Promoter Sequence.