A signal–noise model for significance analysis of ChIP-seq with negative control

摘要

Motivation:ChIP-seq is becoming the main approach to the genome-wide study of protein–DNA interactions and histone modifications. Existing informatics tools perform well to extract strong ChIP-enriched sites. However, two questions remain to be answered: (i) to which extent is a ChIP-seq experiment able to reveal the weak ChIP-enriched sites? (ii) are the weak sites biologically meaningful? To answer these questions, it is necessary to identify the weak ChIP signals from background noise.