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. 2006 Mar;140(3):818-29.
doi: 10.1104/pp.105.072280.

AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks

Saranyan K Palaniswamy  1 , Stephen James, Hao Sun, Rebecca S Lamb, Ramana V Davuluri, Erich Grotewold
Affiliations

AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks

Saranyan K Palaniswamy et al. Plant Physiol. 2006 Mar.

Abstract

Gene regulatory pathways converge at the level of transcription, where interactions among regulatory genes and between regulators and target genes result in the establishment of spatiotemporal patterns of gene expression. The growing identification of direct target genes for key transcription factors (TFs) through traditional and high-throughput experimental approaches has facilitated the elucidation of regulatory networks at the genome level. To integrate this information into a Web-based knowledgebase, we have developed the Arabidopsis Gene Regulatory Information Server (AGRIS). AGRIS, which contains all Arabidopsis (Arabidopsis thaliana) promoter sequences, TFs, and their target genes and functions, provides the scientific community with a platform to establish regulatory networks. AGRIS currently houses three linked databases: AtcisDB (Arabidopsis thaliana cis-regulatory database), AtTFDB (Arabidopsis thaliana transcription factor database), and AtRegNet (Arabidopsis thaliana regulatory network). AtTFDB contains 1,690 Arabidopsis TFs and their sequences (protein and DNA) grouped into 50 (October 2005) families with information on available mutants in the corresponding genes. AtcisDB consists of 25,806 (September 2005) promoter sequences of annotated Arabidopsis genes with a description of putative cis-regulatory elements. AtRegNet links, in direct interactions, several hundred genes with the TFs that control their expression. The current release of AtRegNet contains a total of 187 (September 2005) direct targets for 66 TFs. AGRIS can be accessed at http://Arabidopsis.med.ohio-state.edu.

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Figures

Figure 1.
Figure 1.
TF family identification process.
Figure 2.
Figure 2.
Display of promoters identified in AtcisDB. A represents experimental promoters, B represents predicted promoters, and C represents curated promoters with binding sites in red indicating them to be present in that specific promoter.
Figure 3.
Figure 3.
T1 and TF2 are direct targets of TF1. T2 is an indirect target of TF1. T1 is a direct target of TF1, and T2 is an indirect target of TF1, as it requires the prior activation (or repression) of TF2.
Figure 4.
Figure 4.
A screen shot of the AtRegNet database and its search results for AG. AG has been shown to directly regulate a number of genes, including other floral homeotic genes.
Figure 5.
Figure 5.
A screen shot of the AtcisDB Web search engine and its corresponding search result pages.
Figure 6.
Figure 6.
A screen shot of the AtTFDB Web search engine and its corresponding search result pages.
See this image and copyright information in PMC

References

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