The Arabidopsis Gene Expression Database

The Arabidopsis Gene Expression Database (AGED) is a specialized bioinformatics resource designed to provide an extensive repository of gene expression data for Arabidopsis thaliana, one of the most widely studied model organisms in plant biology. This database compiles, organizes, and visualizes transcriptomic data from various experimental conditions, allowing researchers to explore gene activity in different tissues, developmental stages, and environmental contexts.

With the increasing availability of large-scale transcriptomic datasets, AGED serves as a crucial tool for functional genomics, gene discovery, and regulatory network analysis. It integrates data from multiple high-throughput technologies, including microarray, RNA sequencing (RNA-seq), and quantitative PCR (qPCR), offering a comprehensive view of gene expression dynamics.

  • Gene Expression Profiles : Browse and compare expression levels of Arabidopsis genes across tissues, organs, and treatments.
  • Interactive Visualization : Graphical tools for visualizing expression trends, heatmaps, and gene co-expression networks.
  • Experimental Data Integration : Incorporates RNA-seq, microarray, and qPCR datasets from publicly available sources.
  • Search and Query Tools : Find gene expression data using gene IDs, keywords, or functional categories.
  • Comparative Analysis : Compare gene expression between different conditions, genotypes, or developmental stages.

Gene Expression and Protein Tools

View expression patterns as electronic fluorescent pictographs or heatmaps, explore promoters, identify protein-protein interactions and more.

Molecualr Markersand Mapping Tools 

Perform Next Generation Mapping, or generate your own markers using our molecular marker tools.

Other Genomic Tools and Widgets

Remove duplicates, perform multi-dimensional Venn analyses, or generate random lists of identifiers.

Comprehensive Gene Expression Profiles

AGED provides detailed expression profiles for thousands of Arabidopsis genes. These profiles are derived from curated experiments and datasets, enabling users to examine expression trends across different biological conditions. The data include:

  • Tissue-specific expression – Expression levels in roots, leaves, flowers, seeds, and other organs.
  • Developmental stage analysis – Expression variation during seed germination, vegetative growth, flowering, and senescence.
  • Environmental response – Changes in gene expression in response to light, temperature, drought, salinity, and other stress conditions.
  • Mutant and transgenic studies – Expression patterns in genetically modified Arabidopsis lines.

Interactive Data Visualization

To enhance usability, AGED offers a suite of visualization tools that allow users to interactively explore gene expression data. These tools include:

  • Heatmaps – Display gene expression intensity across different samples.
  • Expression graphs – Line and bar charts showing changes in gene expression over time or under various treatments.
  • Co-expression networks – Graphical representations of genes with similar expression patterns, aiding in functional annotation and pathway discovery.

Advanced Search and Query Tools

AGED is equipped with powerful search functions that allow users to easily retrieve gene expression data using:

  • Gene identifiers (AGI codes, locus names, or TAIR IDs)
  • Functional keywords (e.g., "photosynthesis", "stress response", "flowering time")
  • GO (Gene Ontology) terms and KEGG pathways
  • Experimental conditions and treatments

Data Integration from Multiple Sources

AGED aggregates data from well-established plant genomics and transcriptomics repositories, including:

  • The Arabidopsis Information Resource (TAIR) – Gene function annotations and experimental metadata.
  • NCBI Gene Expression Omnibus (GEO) – Publicly available expression datasets from RNA-seq and microarray experiments.
  • ArrayExpress – A repository for functional genomics data from the European Bioinformatics Institute (EBI).
  • Plant Genomics Databases – Integration with resources such as the Arabidopsis eFP Browser and BAR (Bio-Analytic Resource).