Pscan-ChIP

Pscan-ChIP constructs genome-wide maps of transcription factor (TF)-bound regions by scanning ChIP-Seq-derived genomic regions to identify TF binding sites and analyze motif enrichment and positional bias.

Key Features:

• Motif Scanning: Scans genomic regions using motif descriptors including position-specific frequency matrices from JASPAR and TRANSFAC.
• Enrichment and Positional Bias Evaluation: Assesses motif enrichment and positional bias within scanned genomic regions.
• Identification of Binding Sites: Identifies binding sites for primary TFs and secondary motifs corresponding to other TFs within the regions.
• Positional Correlation Analysis: Analyzes positional correlations among binding sites of different TFs.

Scientific Applications:

• Gene Regulation: Enables analysis of transcription factor dynamics and cooperative interactions through motif and positional correlation analyses at genomic scale.

Methodology:

Pscan-ChIP scans ChIP-Seq-derived genomic regions with predefined or user-uploaded motif descriptors (position-specific frequency matrices such as JASPAR or TRANSFAC), assesses motif enrichment and positional bias, identifies TF binding sites and secondary motifs, and analyzes positional correlations among binding sites.