Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites
نویسندگان
چکیده
منابع مشابه
Using Sequence-Specific Chemical and Structural Properties of DNA to Predict Transcription Factor Binding Sites
An important step in understanding gene regulation is to identify the DNA binding sites recognized by each transcription factor (TF). Conventional approaches to prediction of TF binding sites involve the definition of consensus sequences or position-specific weight matrices and rely on statistical analysis of DNA sequences of known binding sites. Here, we present a method called SiteSleuth in w...
متن کاملIntegrating genomic data to predict transcription factor binding.
Transcription factor binding sites (TFBS) in gene promoter regions are often predicted by using position specific scoring matrices (PSSMs), which summarize sequence patterns of experimentally determined TF binding sites. Although PSSMs are more reliable than simple consensus string matching in predicting a true binding site, they generally result in high numbers of false positive hits. This stu...
متن کاملIncorporating Nucleosome Occupancy to Predict Transcription Factor Binding Sites
Bo Jiang April 29, 2007 ABSTRACT Traditional methods to identify potential binding sites of known transcription factors usually neglect abundant information hidden in a large genomic scale. Recent researches, however, reveal that the intrinsic nucleosome organization in genome can be predicted and may help in directing transcription factors towards their target sites. In this paper, we present ...
متن کاملIntegrating multiple evidence sources to predict transcription factor binding in the human genome.
Information about the binding preferences of many transcription factors is known and characterized by a sequence binding motif. However, determining regions of the genome in which a transcription factor binds based on its motif is a challenging problem, particularly in species with large genomes, since there are often many sequences containing matches to the motif but are not bound. Several rul...
متن کاملA Statistical Method for Finding Transcription Factor Binding Sites
Understanding the mechanisms that determine the regulation of gene expression is an important and challenging problem. A fundamental subproblem is to identify DNA-binding sites for unknown regulatory factors, given a collection of genes believed to be coregulated, and given the noncoding DNA sequences near those genes. We present an enumerative statistical method for identifying good candidates...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2020
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gkaa1134