A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites
نویسندگان
چکیده
منابع مشابه
A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites
MOTIVATION Modern experimental methods provide substantial information on protein-DNA recognition. Studying arrangements of transcription factor binding sites (TFBSs) of interacting transcription factors (TFs) advances understanding of the transcription regulatory code. RESULTS We constructed binding motifs for TFs forming a complex with HIF-1α at the erythropoietin 3(')-enhancer. Correspondi...
متن کاملА Deeper Look Into Transcription Regulatory Code By Preferred Pair Distance Templates For Transcription Factor Binding Sites
Motivation: Modern experimental methods provide substantial information on protein-DNA recognition. Studying arrangements of transcription factor binding sites (TFBS) of interacting transcription factors advances understanding of the transcription regulatory code. Results: We constructed binding motifs for transcription factors forming a complex with HIF-1α at the erythropoietin 3’-enhancer. Co...
متن کاملPseudocounts for transcription factor binding sites
To represent the sequence specificity of transcription factors, the position weight matrix (PWM) is widely used. In most cases, each element is defined as a log likelihood ratio of a base appearing at a certain position, which is estimated from a finite number of known binding sites. To avoid bias due to this small sample size, a certain numeric value, called a pseudocount, is usually allocated...
متن کاملEvolution of transcription factor DNA binding sites.
In bioinformatics, binding of transcription regulatory factors to the cognate binding sites is usually described by sequence-specific binding energy, which is estimated from a training sample of sites. This model implies that all binding sites with binding energy above some threshold are functional and site sequence variations should be considered neutral until they do not reduce this energy be...
متن کاملInformation Content in Transcription Factor Binding Sites
The application of Information Theory to the analysis of genomic sequences and, specifically, transcription factor binding sites, is one of the most successful attempts at modeling the behavior and evolution of these genomic elements. As such, information theory models lie at the core of many transcription factor binding site search and motif discovery tools, such as the widely used Virtual Foo...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2011
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/btr453