Principles of ChIP-seq Data Analysis Illustrated with Examples

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) is a powerful method to determine how transcription factors and other chromatin-associated proteins interact with DNA in order to regulate gene transcription. A single ChIP-seq experiment produces large amounts of highly reproducible data. The challenge is to extract knowledge from the data by thoughtful application of appropriate bioinformatics tools. Here we present a concise introduction into ChIP-seq data analysis in the form of a tutorial based on tools developed by our group. We expose biological questions, explain methods and provide guidelines for the interpretation of the results. While this article focuses on ChIP-seq, most of the algorithms and tools we present are applicable to other chromatin profiling assays based on next generation sequencing (NGS) technology as well.


Editor(s):
Ortuno, F
Rojas, I
Published in:
Proceedings Iwbbio 2014: International Work-Conference On Bioinformatics And Biomedical Engineering, Vols 1 And 2, 682-694
Presented at:
2nd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO), Granada, SPAIN, APR 07-09, 2014
Year:
2014
Publisher:
Granada, Copicentro Granada S L
ISBN:
978-84-15814-84-9
Keywords:
Laboratories:




 Record created 2015-02-20, last modified 2018-03-17


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