ChIPdig

ChIPdig analyzes multi-sample Chromatin Immunoprecipitation sequencing (ChIP-seq) datasets to identify, annotate, and compare genomic enrichment of transcription factor binding and histone modifications.

Key Features:

• Multi-Sample Analysis: Processes multiple ChIP-seq datasets simultaneously for comparative analyses across conditions or experimental designs.
• Genome-wide Differential Enrichment Analysis: Performs genome-wide differential enrichment analysis to identify differences in signal between samples.
• Read Mapping: Aligns sequencing reads to a reference genome.
• Peak Calling: Identifies regions of significant enrichment corresponding to potential protein-DNA interactions.
• Annotation of Regions: Annotates peaks to genomic features including transcription start and termination sites, exons, introns, and untranslated regions (UTRs).
• Visualization Tools: Generates heatmaps and metaplots to visualize coverage and enrichment patterns across genomic regions.

Scientific Applications:

• Epigenetic Research: Mapping transcription factor binding sites and histone modifications to study chromatin regulation.
• Regulatory Mechanism Analysis: Supporting studies that elucidate regulatory mechanisms underlying gene expression changes across different biological conditions or treatments.
• Large-scale ChIP-seq Projects: Enabling processing and comparative analysis of datasets from large-scale projects such as modENCODE.

Methodology:

Performs read mapping to a reference genome, peak calling to detect enriched regions, annotation of peaks to genomic features (transcription start and termination sites, exons, introns, UTRs), generation of heatmaps and metaplots, and genome-wide differential enrichment analysis across multiple samples.