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

Abstract

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 (arabidopsis.med.ohio-state.edu) 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 (grassius.org) 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
Pages61-64
Number of pages4
DOIs
StatePublished - Nov 2 2009
Event2009 Ohio Collaborative Conference on Bioinformatics, OCCBIO 2009 - Cleveland, OH, United States
Duration: Jun 15 2009Jun 17 2009

Other

Other2009 Ohio Collaborative Conference on Bioinformatics, OCCBIO 2009
CountryUnited States
CityCleveland, OH
Period6/15/096/17/09

Keywords

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

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

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