Discovery of regulatory networks in plants by linking promoter and transcription factor databases

Alper Yilmaz*, Saranyan Palaniswamy, Ramana Davuluri, Erich Grotewold

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contribution


Transcription factors (TFs) control the levels as well as the sites and times of expression of a discrete set of target genes by binding to specific cis-regulatory elements in the corresponding promoter regions. They can function as master control switches for the regulation of metabolic pathways, cell differentiation and the cell cycle. Thus, the state of a living cell is the result of regulated transcription of thousands of genes in which TFs are major players. A first step in the discovering the regulatory networks is to establish the organization of cis-elements in promoters and the direct targets of TFs. Towards this goal, our lab has developed two publicly available TF and promoter databases. AGRIS ( is dedicated to reveal regulatory networks in Arabidopsis and is currently composed of databases of putative cis-elements (AtcisDB) and TFs (AtTFDB). The regulatory network in Arabidopsis is constructed based on available data by linking cis-regulatory elements and transcription factors, interactions that are visualized by AtRegNet. GRASSIUS ( provides regulatory information gathered from computational and experimental sources for the grasses, initially including maize, rice, sorghum and sugarcane. Promoter sequences across these grasses and cis-elements important for gene expression are gathered in GrassPROMDB. GrassTFDB contains information on TFs, their DNA-binding properties and the genes that they have been experimentally demonstrated to bind/regulate. GrassREGNET is the ultimate component of GRASSIUS, currently under development, and will provide a dynamic relationship between the contents of GrassTFDB and GrassPROMDB in the light of experimentally verified interactions, helping visualize spatio-temporal gene regulation and regulatory networks.

Original languageEnglish (US)
Title of host publicationOCCBIO'09
Subtitle of host publication2009 Ohio Collaborative Conference on Bioinformatics
Number of pages4
StatePublished - Nov 2 2009
Event2009 Ohio Collaborative Conference on Bioinformatics, OCCBIO 2009 - Cleveland, OH, United States
Duration: Jun 15 2009Jun 17 2009


Other2009 Ohio Collaborative Conference on Bioinformatics, OCCBIO 2009
Country/TerritoryUnited States
CityCleveland, OH


  • Cis-regulatory element
  • Gene regulatory network
  • Plant biology
  • Promoter
  • Transcription factor

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics


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