AGRIS

AGRIS provides integrated databases (AtTFDB, AtcisDB, AtRegNet) for the annotation and analysis of transcription factors, cis-regulatory elements, and gene regulatory networks in Arabidopsis thaliana.

Key Features:

• AtTFDB (Arabidopsis Transcription Factor Database): Provides comprehensive information on transcription factors in Arabidopsis thaliana, including TF families, structural annotations, functional information, and data to identify TF–DNA interactions.
• AtcisDB (Arabidopsis cis-Regulatory Elements Database): Contains predicted and experimentally verified cis-regulatory elements in the Arabidopsis genome with annotations linking CREs to gene expression and transcription factor binding.
• AtRegNet (Arabidopsis Regulatory Network Database): Maps interactions between transcription factors and cis-regulatory elements to represent regulatory networks and provides network visualization via the ReIN application.

Scientific Applications:

• Gene Regulatory Network Analysis: Construction and analysis of gene regulatory networks in Arabidopsis thaliana using mapped TF–CRE interactions.
• Transcription Factor Research: Characterization of TF families, structures, functions, and TF–DNA interactions to study roles in development and stress responses.
• Cis-regulatory Element Studies: Investigation of predicted and experimentally validated CREs to study gene regulation and regulatory element evolution.

Methodology:

Combines computational prediction and curation of experimental data to compile AtTFDB, AtcisDB, and AtRegNet, with integration of network visualization via the ReIN application.