Integrating quantitative information from ChIP-chip experiments into motif finding
نویسندگان
چکیده
منابع مشابه
Integrating quantitative information from ChIP-chip experiments into motif finding.
Identifying binding locations of transcription factors (TFs) within long segments of noncoding DNA is a challenging task. Recent chromatin immunoprecipitation on microarray (ChIP-chip) experiments utilizing tiling arrays are especially promising for this task since they provide high-resolution genome-wide maps of the interactions between the TFs and the DNA. Data from these experiments are inva...
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We present a method for inference of transcriptional modules from heterogeneous data sources. It allows identifying the responsible set of regulators in combination with their corresponding DNA recognition sites (motifs) and target genes. Our approach distinguishes itself from previous work in literature because it fully exploits the knowledge of three independently acquired data sources: ChIP-...
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Identification of DNA motifs from ChIP-seq/ChIP-chip [chromatin immunoprecipitation (ChIP)] data is a powerful method for understanding the transcriptional regulatory network. However, most established methods are designed for small sample sizes and are inefficient for ChIP data. Here we propose a new k-mer occurrence model to reflect the fact that functional DNA k-mers often cluster around ChI...
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MOTIVATION Building an accurate binding model for a transcription factor (TF) is essential to differentiate its true binding targets from those spurious ones. This is an important step toward understanding gene regulation. RESULTS This paper describes a boosting approach to modeling TF-DNA binding. Different from the widely used weight matrix model, which predicts TF-DNA binding based on a li...
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ژورنال
عنوان ژورنال: Biostatistics
سال: 2007
ISSN: 1465-4644,1468-4357
DOI: 10.1093/biostatistics/kxm014