Tree-Based Position Weight Matrix Approach to Model Transcription Factor Binding Site Profiles
نویسندگان
چکیده
منابع مشابه
Tree-Based Position Weight Matrix Approach to Model Transcription Factor Binding Site Profiles
Most of the position weight matrix (PWM) based bioinformatics methods developed to predict transcription factor binding sites (TFBS) assume each nucleotide in the sequence motif contributes independently to the interaction between protein and DNA sequence, usually producing high false positive predictions. The increasing availability of TF enrichment profiles from recent ChIP-Seq methodology fa...
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Regulatory sequence detection is a fundamental challenge in computational biology. The transcription process in protein synthesis starts with the binding of the transcription factor (TF) to its binding site. These binding sites are short DNA segments that are called motifs. Different sites can bind to the same factor. This variability in binding sequences besides their low information content a...
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BACKGROUND Identifying transcription factor binding sites (TFBS) in silico is key in understanding gene regulation. TFBS are string patterns that exhibit some variability, commonly modelled as "position weight matrices" (PWMs). Though convenient, the PWM has significant limitations, in particular the assumed independence of positions within the binding motif; and predictions based on PWMs are u...
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Inferring the combinatorial regulatory code of transcription factors (TFs) from genome-wide TF binding profiles is challenging. A major reason is that TF binding profiles significantly overlap and are therefore highly correlated. Clustered occurrence of multiple TFs at genomic sites may arise from chromatin accessibility and local cooperation between TFs, or binding sites may simply appear clus...
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Identification of transcription factor binding sites within regulatory segments of genomic DNA is an important step toward understanding of the regulatory circuits that control expression of genes. Here, we describe a novel bioinformatics method that bases classification of potential binding sites explicitly on the estimate of sequence-specific binding energy of a given transcription factor. Th...
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ژورنال
عنوان ژورنال: PLoS ONE
سال: 2011
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0024210