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Integrative Analysis of ChIP-Chip and ChIP-Seq Dataset

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Book cover Tiling Arrays

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1067))

Abstract

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.

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Acknowledgment

I would like to thank Dr. Michael Brodsky at Program in Gene Function and Expression in University of Massachusetts Medical School for his critical review of the manuscript and his excellent suggestions.

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Authors and Affiliations

  1. Program in Gene Function and Expression; Program in Bioinformatics and Integrated Biology; Program in Molecular Medicine, University of Massachusetts – Medical School, Worcester, MA, USA

    Lihua Julie Zhu

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  1. Lihua Julie Zhu
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Editor information

Editors and Affiliations

  1. Rm 624A Area 39, The Chinese University of Hong Kong Reproduction, Development and Endocrinol, Hong Kong, China, People's Republic

    Tin-Lap Lee

  2. Rm 624A Area 39, The Chinese University of Hong Kong Reproduction, Development and Endocrinol, Hong Kong, China, People's Republic

    Alfred Chun Shui Luk

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Zhu, L.J. (2013). Integrative Analysis of ChIP-Chip and ChIP-Seq Dataset. In: Lee, TL., Shui Luk, A. (eds) Tiling Arrays. Methods in Molecular Biology, vol 1067. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-607-8_8

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  • DOI: https://doi.org/10.1007/978-1-62703-607-8_8

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-606-1

  • Online ISBN: 978-1-62703-607-8

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