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Unformatted text preview: 1 1 ChIP-chip data analysis Peng Liu 4/24/2008 2 Tiling Microarray Liu, X. S. (2007), Getting Started in Tiling Microarray Analysis, PLoS Computational Biology The availability of sequenced genomes allows commercial tiling microarrays that have probes covering the entire genome. Currently three commercial sources provide tiling microarrays with different probe lengths and spacing: Affymetrix NimbleGen Agilent 3 Application ChIP-chip (Chromatin ImmunoPrecipitation followed by microarray) MeDIP-chip (MethylDNA immunoprecipitation followed by microarray) DNase-Chip Nucleosome Localization ArrayCGH and Copy Number Variation Transcriptome Mapping Maybe more 4 ChIP-chip experiment (Figure 1 from Gottardo et al, Biometrics, 2007) 5 Difference between ChIp-chip and gene expression array Higher dimensions millions of probes More information about probes location on chromatin Different goal map the genome-wide binding regions of transcription factors or other DNA-...
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- Spring '08