Abstract
With the advent of ultra-high-throughput sequencing technologies, ChIP-seq is becoming the main stream for the genome-wide studies of transcription factor binding sites (TFBSs) and histone modification sites. Computational analysis of ChIP-seq data is important for ChIP-seq applications. In this chapter, we first give an overview of the stateof- the-art ChIP-seq analysis tools developed for predicting ChIP-enriched genomic sites. Next, we describe the methods employed in a comprehensive analysis on Chen et al.'s ChIP-seq dataset in mouse embryonic stem cells (mESC) [1]. These methods include the prediction of transcription factor binding peaks, as well as subsequent analysis procedures such as de novo motif-finding and the discovery of transcription factor co-localization. By this, we demonstrate how the computational approaches assist to achieve novel biological discoveries from large-scale ChIP-seq dataset.
Original language | English (US) |
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Title of host publication | Computational Biology of Embryonic Stem Cells |
Publisher | Bentham Science Publishers Ltd. |
Pages | 216-229 |
Number of pages | 14 |
ISBN (Print) | 9781608054343 |
DOIs | |
State | Published - 2012 |
Externally published | Yes |
Keywords
- ChIP-enriched loci
- ChIP-seq
- Chromatin immuno-precipitation
- Computational analysis
- Control library
- Hidden markov model
- Histone modification
- MESC
- Poisson distribution
- Sequencing
- Transcriptional regulation
ASJC Scopus subject areas
- General Biochemistry, Genetics and Molecular Biology