Improved ChIP-chip analysis by a mixture model approach
نویسندگان
چکیده
منابع مشابه
ChIPmix: mixture model of regressions for two-color ChIP-chip analysis
MOTIVATION Chromatin immunoprecipitation (ChIP) combined with DNA microarray is a high-throughput technology to investigate DNA-protein binding or chromatin/histone modifications. ChIP-chip data require adapted statistical method in order to identify enriched regions. All methods already proposed are based on the analysis of the log ratio (Ip/Input). Nevertheless, the assumption that the log ra...
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ChIP-chip (or ChIP-on-chip) is a technology for isolation and identification of genomic sites occupied by specific DNA-binding proteins in living cells. The ChIP-chip signals can be obtained over the whole genome by tiling arrays, where a peak shape is generally observed around a protein-binding site. In this article, we describe the ChIP-chip process and present a probability model for ChIP-ch...
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Chromatin immunoprecipitation (ChIP), followed by high-throughput DNA sequencing (ChIP-seq), enables genome-wide mapping of transcription-factor binding sites (TFBS). Several transcription factors (TFs) have been known to be able to differentiate tumor sub-types in diseases like cancer. For instance, the Luminal A and Luminal B sub-types of breast cancer tumors are high in estrogen receptor (ER...
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The access of transcription factors and the replication machinery to DNA is regulated by the epigenetic state of chromatin. In eukaryotes, this complex layer of regulatory processes includes the direct methylation of DNA, as well as covalent modifications to histones. Using next-generation sequencers, it is now possible to obtain profiles of epigenetic modifications across a genome using chroma...
متن کاملModel-based analysis of tiling-arrays for ChIP-chip.
We propose a fast and powerful analysis algorithm, titled Model-based Analysis of Tiling-arrays (MAT), to reliably detect regions enriched by transcription factor chromatin immunoprecipitation (ChIP) on Affymetrix tiling arrays (ChIP-chip). MAT models the baseline probe behavior by considering probe sequence and copy number on each array. It standardizes the probe value through the probe model,...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2009
ISSN: 1471-2105
DOI: 10.1186/1471-2105-10-173