Introduction

ChIP-chip is a microarray based technology for determining the genomic locations of chromatin bound factors of interest, such as proteins. Standard ChIP-chip analyses employ peak detection methodologies to generate lists of genomic binding sites. No previously published method exists to enable comparative analyses of enrichment levels derived from datasets examining different experimental conditions. This restricts the use of the technology to binary comparisons of presence or absence of features between datasets. Here we present the R package Sandcastle — Software for the Analysis and Normalisation of Data from ChIP-chip AssayS of Two or more Linked Experiments — which allows for comparative analyses of data from multiple experiments by normalising all datasets to a common background. Relative changes in binding levels between experimental datasets can thus be determined, enabling the extraction of latent information from ChIP-chip experiments. Novel enrichment detection and peak calling algorithms are also presented, with a range of graphical tools, which facilitate these analyses. The software and documentation are available for download from http://reedlab.cardiff.ac.uk/sandcastle.

Publications

  1. Sandcastle: software for revealing latent information in multiple experimental ChIP-chip datasets via a novel normalisation procedure.
    Cite this
    Bennett M, Evans KE, Yu S, Teng Y, Webster RM, Powell J, Waters R, Reed SH, 2015-08-01 - Scientific reports

Credits

  1. Mark Bennett
    Developer

    Cancer and Genetics Building, Cardiff University

  2. Katie Ellen Evans
    Developer

    Cancer and Genetics Building, Cardiff University

  3. Shirong Yu
    Developer

    Cancer and Genetics Building, Cardiff University

  4. Yumin Teng
    Developer

    Cancer and Genetics Building, Cardiff University

  5. Richard M Webster
    Developer

    Cancer and Genetics Building, Cardiff University

  6. James Powell
    Developer

    Cancer and Genetics Building, Cardiff University

  7. Raymond Waters
    Developer

    Cancer and Genetics Building, Cardiff University

  8. Simon H Reed
    Investigator

    Cancer and Genetics Building, Cardiff University

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Summary
AccessionBT006572
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted BySimon H Reed