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Circadian Rhythms and Gene Regulation

Circadian Rhythms and Gene Regulation

The biological clock is involved in many aspects of regulating complex physiology in all animals. It was in 1935 when German zoologists, Hans Kalmus and Erwin Bünning, discovered the existence of circadian rhythm in Drosophila melanogaster. However, the internal molecular mechanisms behind the circadian clock remained a mystery until 1984, when Jeffrey C. Hall, Michael Rosbash, and Michael W. Young discovered the expression of the Per gene oscillating over a 24-hour cycle. In subsequent years,...

Circadian Rhythms and Gene Regulation

Circadian Rhythms and Gene Regulation

The biological clock is involved in many aspects of regulating complex physiology in all animals. It was in 1935 when German zoologists, Hans Kalmus and Erwin Bünning, discovered the existence of circadian rhythm in Drosophila melanogaster. However, the internal molecular mechanisms behind the circadian clock remained a mystery until 1984, when Jeffrey C. Hall, Michael Rosbash, and Michael W. Young discovered the expression of the Per gene oscillating over a 24-hour cycle. In subsequent years,...

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Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

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The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.

T C Mockler¹, T P Michael, H D Priest

¹Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA.

Cold Spring Harbor Symposia on Quantitative Biology

|April 19, 2008

Summary

The DIURNAL project offers tools to analyze plant gene expression patterns, aiding in the discovery of co-regulated genes and regulatory elements. This facilitates cross-species comparisons and advances functional genomics research.

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Area of Science:

Plant biology
Genomics
Bioinformatics

Background:

Diurnal and circadian rhythms significantly influence gene expression in plants.
Analyzing large-scale microarray data is crucial for understanding gene regulation.
Comparative genomics across species aids in functional gene discovery.

Purpose of the Study:

To introduce the DIURNAL project, a graphical interface for analyzing plant diurnal and circadian microarray data.
To present associated tools, HAYSTACK and ELEMENT, for gene co-expression analysis and cis-regulatory element identification.
To enable cross-species functional genomics research in Arabidopsis, poplar, and rice.

Main Methods:

Development of a searchable database with user-friendly web-based data-mining tools.
Application of the HAYSTACK algorithm for model-based pattern matching of gene expression.
Utilization of the ELEMENT program for identifying cis-regulatory elements in gene promoters.

Main Results:

DIURNAL provides access to mining and viewing diurnal and circadian microarray data.
HAYSTACK identifies coexpressed and potentially coregulated genes using user-defined patterns.
ELEMENT identifies potential cis-regulatory elements in coregulated genes across multiple plant species.

Conclusions:

The DIURNAL project, HAYSTACK, and ELEMENT collectively support cross-species comparisons.
These integrated tools accelerate functional genomics research by simplifying data analysis and discovery.
The project enhances the study of diurnal and circadian gene regulation in plants.