Motif2Site

Motif2Site detects binding sites using motif IUPAC sequences or bed coordinates with ChIP-seq experiments in bed or bam format, and combines or compares binding sites across experiments, tissues, or conditions.

Key Features:

• Motif-based binding site detection: Detects binding sites using motifs provided as IUPAC sequences or bed coordinates.
• ChIP-seq data support: Processes ChIP-seq experiments in bed or bam format.
• Cross-condition comparison: Combines and compares binding sites across experiments, tissues, or conditions.
• Normalization and differential analysis: Performs all normalization and differential steps using the TMM-GLM method.
• Signal decomposition: Decomposes signal by setting motifs as the centers of the mixture of normal distribution curves.

Scientific Applications:

• ChIP-seq binding site identification: Identifies transcription factor binding sites from motif sequences and ChIP-seq data.
• Cross-tissue or cross-condition binding analysis: Compares binding site landscapes across different biological conditions or tissues.
• Differential binding analysis: Detects differential binding sites using TMM-GLM normalization and statistical testing.

Methodology:

All normalization and differential steps are done using TMM-GLM method. Signal decomposition is done by setting motifs as the centers of the mixture of normal distribution curves.