MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data
نویسندگان
چکیده
منابع مشابه
Epigenetic 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 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 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 کاملImpact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data
With the advent of ChIP-seq multiplexing technologies and the subsequent increase in ChIP-seq throughput, the development of working standards for the quality assessment of ChIP-seq studies has received significant attention. The ENCODE consortium's large scale analysis of transcription factor binding and epigenetic marks as well as concordant work on ChIP-seq by other laboratories has establis...
متن کاملChIP-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...
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ژورنال
عنوان ژورنال: Genome Biology
سال: 2011
ISSN: 1465-6906
DOI: 10.1186/gb-2011-12-2-r11