RSEG_USC

The RSEG method is presented as a software tool that identifies epigenomic domains from ChIP-Seq data for histone modifications.

Post-translational modifications to histones have several well-known associations with the regulation of gene expression. While some modifications appear concentrated narrowly, covering promoters or enhancers, others are dispersed as epigenomic domains. These domains mark contiguous regions sharing an epigenomic property, such as actively transcribed or poised genes or hetero-chromatically silenced regions. The high-throughput methods like ChIP-Seq have led to a flood of high-quality data about these epigenomic domains. However, there remain essential analysis problems that are not adequately solved by current analysis tools.

In contrast with other methods emphasizing the locations of 'peaks' in read density profiles, the RSEG method identifies the boundaries of domains. Doing so provides a better understanding of the domains and their characteristics. Additionally, RSEG can incorporate a control sample, allowing researchers to find the differential histone modifications between two samples. This is a significant advantage, as it can provide valuable information on gene expression that is not apparent in other methods.

A significant challenge in analyzing ChIP-Seq data is the high level of noise and the large amount of data generated. The RSEG method has been designed to address these challenges, providing a more accurate and efficient analysis of the data. This is especially important as the amount of data generated by ChIP-Seq continues to increase, making it more challenging to analyze and interpret.