ABS

ABS provides a curated database of experimentally validated transcription factor binding sites in promoters of orthologous vertebrate genes (human, mouse, rat, chicken) to support comparative gene regulation and motif analysis.

Key Features:

• Curated Data Collection: ABS contains 650 experimentally validated binding sites associated with 68 transcription factors and 100 orthologous target genes curated from the scientific literature.
• Orthologous Promoter Analysis: The resource focuses on promoters of orthologous vertebrate genes to enable identification of conserved regulatory elements across species.
• Comprehensive Annotations: Each entry includes genomic coordinates, sequence information, computational predictions, and promoter alignments.
• Customizable Artificial Datasets: Release 1.0 provides generation of artificial datasets derived from known binding sites for training and evaluating motif-finding algorithms.
• Evaluation Tool: The database includes an evaluation tool to assess the performance of computational methods for identifying transcription factor binding motifs.

Scientific Applications:

• Motif Discovery and Validation: Support for development, training, and benchmarking of computational motif-finding and validation methods using experimentally validated sites and artificial datasets.
• Comparative Genomics: Analysis of orthologous promoters across human, mouse, rat, and chicken to study evolutionary conservation and divergence of regulatory elements.
• Gene Regulation Research: Investigation of the distribution and functional roles of transcription factor binding sites in promoter regions across vertebrate species.

Methodology:

Data were manually curated from the scientific literature; the database incorporates computational predictions and promoter sequence alignments.