Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments

Background: High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ensures consistent sampling across coding and non-coding regions of the genome. Tiling arrays are increasingly used in chromatin immunoprecipitation (IP) experiments (ChIP on chip). ChIP on chip facilitates the generation of genome-wide maps of in-vivo interactions between DNA-associated proteins including transcription factors and DNA. Analysis of the hybridization of an immunoprecipitated sample to a tiling array facilitates the identification of ChIPenriched segments of the genome. These enriched segments are putative targets of antibody assayable regulatory elements. The enrichment response is not ubiquitous across the genome. Typically 5 to 10% of tiled probes manifest some significant enrichment. Depending upon the factor being studied, this response can drop...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Srinka Ghosh, Heather A. Hirsch, Edward A. Sekinger, Kevin Struhl, Thomas R. Gingeras
• Keywords: BMCBI 2006, Chip, Genome, Unbiased Genome-wide Studies