Understanding Variation in Transcription Factor Binding by Modeling Transcription Factor Genome-Epigenome Interactions
نویسندگان
چکیده
منابع مشابه
Understanding Variation in Transcription Factor Binding by Modeling Transcription Factor Genome-Epigenome Interactions
Despite explosive growth in genomic datasets, the methods for studying epigenomic mechanisms of gene regulation remain primitive. Here we present a model-based approach to systematically analyze the epigenomic functions in modulating transcription factor-DNA binding. Based on the first principles of statistical mechanics, this model considers the interactions between epigenomic modifications an...
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Differences in gene expression may play a major role in speciation and phenotypic diversity. We examined genome-wide differences in transcription factor (TF) binding in several humans and a single chimpanzee by using chromatin immunoprecipitation followed by sequencing. The binding sites of RNA polymerase II (PolII) and a key regulator of immune responses, nuclear factor kappaB (p65), were mapp...
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Recent experimental and theoretical efforts have highlighted the fact that binding of transcription factors to DNA can be more accurately described by continuous measures of their binding affinities, rather than a discrete description in terms of binding sites. While the binding affinities can be predicted from a physical model, it is often desirable to know the distribution of binding affiniti...
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Motivation: Generating small models for which there may exist very little training data presents a crucial problem in computational biology, namely the trade-oo between model speciicity and under-tting the data. There are a bevy of superior modeling techniques; however, certain domain speciic problems, such as modeling the regulatory regions in intergenic DNA impose constraints on the modeling ...
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One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies...
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ژورنال
عنوان ژورنال: PLoS Computational Biology
سال: 2013
ISSN: 1553-7358
DOI: 10.1371/journal.pcbi.1003367