MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data
نویسندگان
چکیده
منابع مشابه
MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data
BACKGROUND As a key mechanism of gene regulation, transcription factors (TFs) bind to DNA by recognizing specific short sequence patterns that are called DNA-binding motifs. A single TF can accept ambiguity within its DNA-binding motifs, which comprise both canonical (typical) and non-canonical motifs. Clarification of such DNA-binding motif ambiguity is crucial for revealing gene regulatory ne...
متن کاملInferring direct DNA binding from ChIP-seq
Genome-wide binding data from transcription factor ChIP-seq experiments is the best source of information for inferring the relative DNA-binding affinity of these proteins in vivo. However, standard motif enrichment analysis and motif discovery approaches sometimes fail to correctly identify the binding motif for the ChIP-ed factor. To overcome this problem, we propose 'central motif enrichment...
متن کاملDREME: motif discovery in transcription factor ChIP-seq data
MOTIVATION Transcription factor (TF) ChIP-seq datasets have particular characteristics that provide unique challenges and opportunities for motif discovery. Most existing motif discovery algorithms do not scale well to such large datasets, or fail to report many motifs associated with cofactors of the ChIP-ed TF. RESULTS We present DREME, a motif discovery algorithm specifically designed to f...
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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: Computational Biology and Chemistry
سال: 2016
ISSN: 1476-9271
DOI: 10.1016/j.compbiolchem.2016.01.014