JAMIE: A software tool for jointly analyzing multiple ChIP-chip experiments

Hao Wu, Hong Kai Ji

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Chromatin immunoprecipitation followed by genome tiling array hybridization (ChIP-chip) is a powerful approach to map transcription factor binding sites (TFBSs). Similar to other high-throughput genomic technologies, ChIP-chip often produces noisy data. Distinguishing signals from noise in these data is challenging. ChIP-chip data in public databases are rapidly growing. It is becoming more and more common that scientists can find multiple data sets for the same transcription factor in different biological contexts or data for different transcription factors in the same biological context. When these related experiments are analyzed together, binding site detection can be improved by borrowing information across data sets. This chapter introduces a computational tool JAMIE for Jointly Analyzing Multiple ChIP-chip Experiments. JAMIE is based on a hierarchical mixture model, and it is implemented as an R package. Simulation and real data studies have shown that it can significantly increase sensitivity and specificity of TFBS detection compared to existing algorithms. The purpose of this chapter is to describe how the JAMIE package can be used to perform the integrative data analysis.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
Pages363-375
Number of pages13
Volume802
DOIs
StatePublished - 2012

Publication series

NameMethods in Molecular Biology
Volume802
ISSN (Print)10643745

Fingerprint

Transcription Factors
Software
Binding Sites
Chromatin Immunoprecipitation
Genome
Databases
Technology
Sensitivity and Specificity
Datasets

Keywords

  • ChIP-chip
  • Data integration
  • Tiling array
  • Transcription factor binding site

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Wu, H., & Ji, H. K. (2012). JAMIE: A software tool for jointly analyzing multiple ChIP-chip experiments. In Methods in Molecular Biology (Vol. 802, pp. 363-375). (Methods in Molecular Biology; Vol. 802). https://doi.org/10.1007/978-1-61779-400-1_24

JAMIE : A software tool for jointly analyzing multiple ChIP-chip experiments. / Wu, Hao; Ji, Hong Kai.

Methods in Molecular Biology. Vol. 802 2012. p. 363-375 (Methods in Molecular Biology; Vol. 802).

Research output: Chapter in Book/Report/Conference proceedingChapter

Wu, H & Ji, HK 2012, JAMIE: A software tool for jointly analyzing multiple ChIP-chip experiments. in Methods in Molecular Biology. vol. 802, Methods in Molecular Biology, vol. 802, pp. 363-375. https://doi.org/10.1007/978-1-61779-400-1_24
Wu H, Ji HK. JAMIE: A software tool for jointly analyzing multiple ChIP-chip experiments. In Methods in Molecular Biology. Vol. 802. 2012. p. 363-375. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-61779-400-1_24
Wu, Hao ; Ji, Hong Kai. / JAMIE : A software tool for jointly analyzing multiple ChIP-chip experiments. Methods in Molecular Biology. Vol. 802 2012. pp. 363-375 (Methods in Molecular Biology).
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