TFmotifView

TFmotifView visualizes transcription factor (TF) motif occurrences and quantifies their enrichment within user-specified genomic regions to analyze TF binding specificity represented by position-weight matrices.

Key Features:

• Motif Overlap Analysis: Performs overlap analysis between user-defined genomic regions and motif occurrences from the JASPAR database using position-weight matrices and a dynamic P-value threshold.
• Enrichment Assessment: Computes enrichment statistics and provides an enrichment table and scatterplot comparing motif occurrence frequencies in target versus control regions.
• Genomic Visualization: Produces a detailed genomic view of motif organization across each region and supports export of motif positions for visualization in the UCSC Genome Browser.
• Metaplot Generation: Generates metaplots summarizing the relative positioning of TF motifs with respect to the center of genomic regions.

Scientific Applications:

• Motif–genome integration: Integrates TF motif information with genomic datasets to characterize regulatory element composition.
• Gene regulation analysis: Identifies statistically significant TF motifs that may contribute to gene expression regulation.
• Spatial distribution studies: Analyzes positional patterns of TF motifs relative to genomic features to inform functional interpretation.

Methodology:

Input user-defined genomic regions and select TF motifs; perform overlap analysis with motif occurrences from the JASPAR database; calculate significance using dynamic P-value thresholds; generate visual outputs including enrichment table, scatterplot, genomic view and metaplot, and export motif positions.