New BAR tools for mining expression data and exploring Cis-elements in Arabidopsis thaliana.

Area of Science:

• * Molecular Biology
• * Bioinformatics
• * Genomics

Background:

• * Identifying genes with specific expression patterns is crucial for various biological applications.
• * Understanding gene regulatory networks requires analyzing gene expression and promoter elements.

Purpose of the Study:

• * To develop user-friendly online tools for identifying genes based on desired expression profiles.
• * To create a tool for predicting and exploring cis-elements in co-expressed gene promoters.
• * To present practical use cases for these bioinformatics tools.

Main Methods:

• * Developed a modified Expression Angler program as an online tool to define and match gene expression profiles.
• * Developed the Cistome online tool for cis-element analysis in gene promoters.
• * Demonstrated tool utility through two distinct use cases.

Main Results:

• * Successfully created online tools for targeted gene identification based on expression patterns.
• * Enabled prediction and exploration of cis-regulatory elements in sets of co-expressed genes.
• * Provided practical examples of the tools' application in biological research.

Conclusions:

• * The developed online tools offer accessible solutions for gene expression analysis and promoter exploration.
• * These tools facilitate advancements in reporter construct design, gene marker development, and gene regulatory network studies.
• * The tools are freely available for researchers on the Bio-Analytic Resource (BAR).