SiteSeer

SiteSeer visualizes transcription factor binding site (TFBS) mappings in upstream promoter regions of eukaryotic genes to support analysis of gene regulation.

Key Features:

• TFBS mapping and visualization: Maps and displays TFBS located upstream of transcriptional start sites on nucleotide sequences.
• Known and user-defined motifs: Accepts and visualizes TFBS from established sources as well as user-defined binding sites.
• Database integration: Integrates motif data from TRANSFAC and SCPD for mapping onto promoter regions.
• Expectation-value filtering: Applies restrictions based on expectation values for specific DNA words and binding sites.
• Organism-specific site handling: Supports filtering and analysis of binding sites unique to particular organisms.
• Analysis of over-represented sequences: Identifies sequences over-represented in sets of co-expressed or functionally related genes, including sequences derived from microarray-based studies.

Scientific Applications:

• Promoter analysis: Examination and annotation of promoter sequences and TFBS upstream of transcriptional start sites.
• Regulatory motif discovery in co-expressed genes: Detection of shared or over-represented TFBS among co-expressed or functionally related gene sets.
• Cross-database motif annotation: Use of TRANSFAC and SCPD motif sets for comparative promoter mapping and hypothesis generation about regulatory control.
• Organism-specific regulatory studies: Investigation of species-specific binding sites and their expected occurrence in promoter regions.

Methodology:

Maps TFBS from TRANSFAC, SCPD, and user-defined motifs onto nucleotide sequences of promoter regions upstream of transcriptional start sites; applies expectation-value-based restrictions for DNA words and organism-specific binding sites; identifies over-represented sequences in sets of co-expressed genes (e.g., from microarray studies).