منابع مشابه
ChIP-Enrich: gene set enrichment testing for ChIP-seq data
Gene set enrichment testing can enhance the biological interpretation of ChIP-seq data. Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene locus length (the length of the gene body and its surrounding non-coding sequence). Adjustment for gene locus length is necessary because it is often positively associated with the presence of one or more peaks and b...
متن کاملNonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data
Chromatin immunoprecipitation sequencing (ChIP-seq) is a powerful method for analyzing protein interactions with DNA. It can be applied to identify the binding sites of transcription factors (TFs) and genomic landscape of histone modification marks (HMs). Previous research has largely focused on developing peak-calling procedures to detect the binding sites for TFs. However, these procedures ma...
متن کاملIdentifying causal regulatory SNPs in ChIP-seq enhancers
Thousands of non-coding SNPs have been linked to human diseases in the past. The identification of causal alleles within this pool of disease-associated non-coding SNPs is largely impossible due to the inability to accurately quantify the impact of non-coding variation. To overcome this challenge, we developed a computational model that uses ChIP-seq intensity variation in response to non-codin...
متن کاملIdentifying dispersed epigenomic domains from ChIP-Seq data
MOTIVATION Post-translational modifications to histones have several well known associations with 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 heterochromatical...
متن کاملIdentifying differential transcription factor binding in ChIP-seq
ChIP seq is a widely used assay to measure genome-wide protein binding. The decrease in costs associated with sequencing has led to a rise in the number of studies that investigate protein binding across treatment conditions or cell lines. In addition to the identification of binding sites, new studies evaluate the variation in protein binding between conditions. A number of approaches to study...
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ژورنال
عنوان ژورنال: Nature Protocols
سال: 2012
ISSN: 1754-2189,1750-2799
DOI: 10.1038/nprot.2012.101