Power Spectrum-Based Genomic Feature Extraction from High-Throughput ChIP-seq Sequences

Abstract

Due to its enhanced accuracy and high-throughput capability in capturing genetic activities, recently Next Generation Sequencing technology is being applied prevalently in biomedical study for tackling diverse topics. Within the work, we propose a computational method for answering such questions as deciding optimal argument pairs (peak number, p-value threshold, selected bin size and false discovery rate) from estrogen receptor α ChIP-seq data, and detecting corresponding transcription factor binding sites. We employ a signal processing-based approach to extract inherent genomic features from the identified transcription factor binding sites, which illuminates novel evidence for further analysis and experimental validation. Thus eventually we attempt to exploit the potentiality of ChIP-seq for deep comprehension of inherent biological meanings from the high-throughput genomic sequences.