ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data
نویسندگان
چکیده
منابع مشابه
MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data
BACKGROUND As a key mechanism of gene regulation, transcription factors (TFs) bind to DNA by recognizing specific short sequence patterns that are called DNA-binding motifs. A single TF can accept ambiguity within its DNA-binding motifs, which comprise both canonical (typical) and non-canonical motifs. Clarification of such DNA-binding motif ambiguity is crucial for revealing gene regulatory ne...
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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...
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ChIP-chip and ChIP-seq are powerful technologies to study transcriptional regulation in complex genomes, however, mining information from the huge datasets generated by these highthroughput technologies remains to be a non-trivial task. To analyze a ChIP-chip experiment, one usually starts with data exploration and then goes through normalization, binding region detection, adding gene annotatio...
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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...
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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...
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ژورنال
عنوان ژورنال: Theoretical Biology and Medical Modelling
سال: 2010
ISSN: 1742-4682
DOI: 10.1186/1742-4682-7-18