Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences

Timothy R O'Connor; Curtis Dyreson; John J Wyrick

doi:10.1093/bioinformatics/bti714

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Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences

Journal article

Open access

Peer reviewed

Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences

Timothy R O'Connor, Curtis Dyreson and John J Wyrick

Bioinformatics (Oxford, England), Vol.21(24), pp.4411-4413

12/15/2005

DOI: https://doi.org/10.1093/bioinformatics/bti714

Handle:

https://hdl.handle.net/2376/107557

PMID: 16223790

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Abstract

Promoter Regions, Genetic

Genes, Plant

Computational Biology

Sequence Analysis, DNA - statistics & numerical data

Binding Sites - genetics

DNA, Plant - metabolism

Arabidopsis - metabolism

Arabidopsis - genetics

Arabidopsis Proteins - metabolism

Transcription Factors - metabolism

Internet

Databases, Nucleic Acid

DNA, Plant - genetics

To better understand the regulatory networks that control plant gene expression, tools are needed to systematically analyze and visualize promoter regulatory sequences in Arabidopsis thaliana. We have developed the Athena database, which contains 30,067 predicted Arabidopsis promoter sequences and consensus sequences for 105 previously characterized transcription factor (TF) binding sites. Athena provides four novel tools to facilitate the analysis of promoter sequences: a promoter visualization tool to enable the rapid inspection of key regulatory sequences in multiple promoters; a TF binding site enrichment tool to identify statistically over-represented TF sites occurring in a user-selected subset of promoters; a data-mining tool to rapidly select promoter sequences containing the specified combination of TF binding sites; and a tool to display the distribution of TF binding site positions in a selected set of promoter sequences.

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Title: Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences
Creators: Timothy R O'Connor - School of Molecular Biosciences, Washington State University, Pullman, WA, USA
Curtis Dyreson
John J Wyrick
Publication Details: Bioinformatics (Oxford, England), Vol.21(24), pp.4411-4413
Academic Unit: Molecular Biosciences, School of
Publisher: England
Identifiers: 99900547122101842
Language: English
Resource Type: Journal article