ACME

ACME identifies enriched regions in high-density oligonucleotide tiling array data to detect genomic loci with significant signal from experiments such as ChIP-chip and DNase-chip.

Key Features:

• Technology-agnostic design: Functions independently of specific tiling array technologies and accepts high-density oligonucleotide tiling array data.
• Robust signal detection: Employs a sliding-window and threshold strategy to detect peaks and assigns per-probe probability values (p-values) for statistical assessment.
• Noise insensitivity: Demonstrates insensitivity to array noise and to variations in normalization methods.
• Efficiency and scalability: Processes whole-genome tiling array experiments efficiently given sufficient computational memory.

Scientific Applications:

• ChIP-chip analysis: Maps protein–DNA interactions by identifying enriched regions from Chromatin Immunoprecipitation microarray (ChIP-chip) experiments.
• DNase-chip analysis: Identifies DNase I hypersensitive sites and regions of open chromatin from DNase-chip experiments.
• Gene regulation and epigenetics: Aids identification of transcription factor binding sites and enriched regions associated with epigenetic modifications to support studies of gene regulation.

Methodology:

Implemented in R; processes raw tiling array data using a sliding-window and threshold peak-detection strategy and assigns p-values to probes to determine statistical significance of enrichment signals.