Authors
Zhu, Lihua JulieUMass Chan Affiliations
Program in Gene Function and ExpressionDocument Type
Book ChapterPublication Date
2013-08-27
Metadata
Show full item recordAbstract
Epigenetic regulation and interactions between transcription factors and regulatory genomic regions play crucial roles in controlling transcriptional regulatory networks that drive development, environmental responses, and disease. Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) and ChIP followed by genomic tiling microarray hybridization (ChIP-chip) are the two of the most widely used technologies for genome-wide identification of DNA protein interactions and histone modification in vivo. Many algorithms and tools have been developed and evaluated that allow identification of transcription factor binding sites from ChIP-seq or ChIP-chip datasets. However, binding site identification is only the first step; the ultimate goal is to discover the regulatory network of the transcription factor (TF). Here, we present a common workflow for downstream analysis of ChIP-chip and ChIP-seq with an emphasis on annotating binding sites and integration with gene expression data to identify direct and indirect targets of the TF. These tools will help with the overall goal of unraveling transcriptional regulatory networks using datasets publicly available in GEO.Source
Methods Mol Biol. 2013;1067:105-24. doi: 10.1007/978-1-62703-607-8_8. Link to article on publisher's siteDOI
10.1007/978-1-62703-607-8_8Permanent Link to this Item
http://hdl.handle.net/20.500.14038/44013PubMed ID
23975789Related Resources
Link to Article in PubMedae974a485f413a2113503eed53cd6c53
10.1007/978-1-62703-607-8_8