CASSys

CASSys performs comprehensive analysis of genome-wide chromatin immunoprecipitation (ChIP) data for both ChIP-chip and ChIP-seq to identify enriched binding regions, compute statistical confidence, analyze regulatory sequence motifs, and leverage massively parallel sequencing technologies.

Key Features:

• Visualization: Visualizes array images, signal tracks, gene structures, conservation elements, DNA sequences, and motif annotations.
• Data Normalization and Peak Detection: Implements data normalization techniques and peak detection algorithms tailored for ChIP-seq and ChIP-chip to identify regions of enrichment.
• False Discovery Rate Computation: Computes false discovery rates for statistical assessment of detected peaks.
• Gene-Peak Association and Motif Analysis: Performs gene-peak association and sequence motif analysis to link peaks to genes and candidate regulatory elements.
• Comparative Analyses: Enables comparative analyses between ChIP-chip and ChIP-seq datasets, as exemplified by studies on the transcription factor NRSF/REST.
• Customization for Advanced Analysis: Provides a modular architecture that supports batch-mode computation for large-scale data mining.

Scientific Applications:

• Transcription Factor Binding Mapping: Mapping transcription factor binding sites such as NRSF/REST across the genome.
• Epigenetic Modification Profiling: Identifying regions of histone modifications and other chromatin marks from ChIP-seq data.
• Gene Regulation Studies: Associating peaks with genes to study regulatory relationships and transcriptional control.
• Cross-Platform Validation: Validating findings across ChIP-chip and ChIP-seq platforms.
• Motif Discovery and Analysis: Discovering and characterizing novel sequence motifs within peak regions, including analyses performed with or without negative control samples.

Methodology:

Implements data normalization, peak detection algorithms, false discovery rate computation, gene-peak association and sequence motif analysis, and comparative analyses between ChIP-chip and ChIP-seq, with support for batch-mode computation.