PromoterPlot

PromoterPlot analyzes transcription factor prediction results to identify conserved promoter patterns and prioritize biologically relevant factors for studies of gene regulation.

Key Features:

• Input Compatibility: Accepts input from TransFac searches or FASTA sequences and Affymetrix IDs and accommodates commercial and free TransFac distributions as well as local TransFac installations.
• Pattern Recognition Algorithm: Divides transcription factor predictions into conserved triplet models to identify similarities between groups of promoters.
• Expression-based Filtering: Optionally excludes factors known to be unexpressed or inactive in the cells under study based on microarray or proteomic expression data to reduce false positives.
• Statistical Estimation: Estimates the likelihood that identified patterns could occur by chance using frequency observed in a control set of mammalian promoters from Genomatix.
• Interactive SVG Visualization: Stores results as interactive SVG visualizations for exploration of transcription factor binding patterns across promoters.

Scientific Applications:

• Gene Regulation Analysis: Identification of conserved promoter patterns and transcription factor interactions to inform studies of regulatory architecture.
• Expression Profiling Integration: Prioritization of transcription factors by integrating microarray and proteomic expression data to focus on biologically active factors.
• Comparative Genomics: Comparison of transcription factor binding site patterns across different promoters to detect conserved regulatory motifs.
• Therapeutic Target Identification: Support for identifying candidate regulatory factors relevant to applied studies and target discovery.

Methodology:

Accepts TransFac search results or FASTA/Affymetrix IDs; divides TF predictions into conserved triplet models via a pattern recognition algorithm; optionally filters factors using microarray or proteomic expression data; estimates significance from frequencies in a control set of mammalian promoters from Genomatix; stores results as interactive SVG visualizations.