Footer

Footer analyzes homologous mammalian promoter sequences to identify transcriptional DNA regulatory signals by detecting high-probability transcription factor binding sites.

Key Features:

• Promoter-focused analysis: Operates specifically on homologous mammalian promoter sequences to locate regulatory signals.
• Pairwise comparative scanning: Analyzes pairs of homologous DNA sequences (for example, human and mouse or rat) to detect conserved binding sites.
• PSSM-based detection: Leverages position-specific scoring matrices (PSSMs) that encode transcription factor binding preferences.
• TRANSFAC-derived models: Constructs PSSM models from known mammalian TF binding sites sourced from the TRANSFAC database.
• Known TF targeting: Identifies high-probability binding sites for known transcription factors.
• Validation on curated sites: Tested on a set of 72 confirmed TF binding sites involving 19 transcription factors, achieving 83% sensitivity and 72% specificity and detecting many sites not previously cataloged in TRANSFAC.

Scientific Applications:

• Comparative genomics: Identification of conserved regulatory elements across mammalian species using pairwise promoter comparisons.
• Functional genomics: Mapping candidate transcription factor binding sites in promoter regions for downstream experimental validation.
• Mammalian gene regulation studies: Analysis of transcription factor binding dynamics across human, mouse, and rat promoters.

Methodology:

Uses position-specific scoring matrices (PSSMs) constructed from TRANSFAC mammalian TF binding sites and analyzes pairs of homologous promoter DNA sequences to identify high-probability transcription factor binding sites.