An integrated ChIP-seq analysis platform with customizable workflows

BMC Bioinformatics
Eugenia Giannopoulou, Olivier Elemento


Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq), enables unbiased and genome-wide mapping of protein-DNA interactions and epigenetic marks. The first step in ChIP-seq data analysis involves the identification of peaks (i.e., genomic locations with high density of mapped sequence reads). The next step consists of interpreting the biological meaning of the peaks through their association with known genes, pathways, regulatory elements, and integration with other experiments. Although several programs have been published for the analysis of ChIP-seq data, they often focus on the peak detection step and are usually not well suited for thorough, integrative analysis of the detected peaks. To address the peak interpretation challenge, we have developed ChIPseeqer, an integrative, comprehensive, fast and user-friendly computational framework for in-depth analysis of ChIP-seq datasets. The novelty of our approach is the capability to combine several computational tools in order to create easily customized workflows that can be adapted to the user's needs and objectives. In this paper, we describe the main components of the ChIPseeqer framework, and also demonstrate the utility and diversity of the analys...Continue Reading


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Related Concepts

ETS1 protein, human
Genome Mapping
Enhancer Elements, Genetic
Computer Programs and Programming
Jurkat Cells
Histone Code
Chromatin Immunoprecipitation
Proto-Oncogene Protein c-ets-1
High-Throughput Nucleotide Sequencing

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