منابع مشابه
ChIP-chip: data, model, and analysis.
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...
متن کاملHierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data
MOTIVATION Chromatin immunoprecipitation (ChIP) experiments followed by array hybridization, or ChIP-chip, is a powerful approach for identifying transcription factor binding sites (TFBS) and has been widely used. Recently, massively parallel sequencing coupled with ChIP experiments (ChIP-seq) has been increasingly used as an alternative to ChIP-chip, offering cost-effective genome-wide coverag...
متن کاملChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data
MOTIVATION Although chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) or tiling array hybridization (ChIP-chip) is increasingly used to map genome-wide-binding sites of transcription factors (TFs), it still remains difficult to generate a quality ChIPx (i.e. ChIP-seq or ChIP-chip) dataset because of the tremendous amount of effort required to develop effective ant...
متن کاملEpigenetic analysis: ChIP-chip and ChIP-seq.
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 کاملStarr: Simple Tiling ARRay analysis for Affymetrix ChIP-chip data
Starr is an extension of the Ringo [6] package for the analysis of ChIP-chip projects. Whereas the latter is specialized to the processing of Nimblegen and Agilent arrays, the former provides all corresponding features for Affymetrix arrays. Data can be read in from Affymetrix CEL-files, or from text files in gff format. Standard quality assessment and data normalization tools are available. St...
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ژورنال
عنوان ژورنال: Biometrics
سال: 2007
ISSN: 0006-341X
DOI: 10.1111/j.1541-0420.2007.00768.x