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Estrogen is a steroid hormone that plays critical roles in a myriad of intracellular pathways. The expression of many genes is regulated through the steroid hormone receptors ESR1 and ESR2. These bind to DNA and modulate the expression of target genes. Identification of estrogen target genes is greatly facilitated by the use of transcriptomic methods, such as RNA-seq and expression microarrays, and chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq). Combining transcriptomic and ChIP-seq data enables a distinction to be drawn between direct and indirect estrogen target genes. This chapter discusses some methods of identifying estrogen target genes that do not require any expertise in programming languages or complex bioinformatics.

Original publication




Journal article


Methods Mol Biol

Publication Date





29 - 39


Bioinformatics, ChIP-seq, Estrogen, Gene target s, Transcriptomics, Animals, Binding Sites, Chromatin Immunoprecipitation, Computational Biology, Databases, Genetic, Estrogen Receptor alpha, Estrogens, Gene Expression Profiling, Gene Expression Regulation, Humans, Oligonucleotide Array Sequence Analysis, Promoter Regions, Genetic, Software, User-Computer Interface, Workflow