SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing.
Identifieur interne : 000397 ( Main/Exploration ); précédent : 000396; suivant : 000398SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing.
Auteurs : Dennis C. Wylie [États-Unis] ; Hans A. Hofmann [États-Unis] ; Boris V. Zemelman [États-Unis]Source :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2019.
Abstract
We set out to develop an algorithm that can mine differential gene expression data to identify candidate cell type-specific DNA regulatory sequences. Differential expression is usually quantified as a continuous score-fold-change, test-statistic, P-value-comparing biological classes. Unlike existing approaches, our de novo strategy, termed SArKS, applies non-parametric kernel smoothing to uncover promoter motif sites that correlate with elevated differential expression scores. SArKS detects motif k-mers by smoothing sequence scores over sequence similarity. A second round of smoothing over spatial proximity reveals multi-motif domains (MMDs). Discovered motif sites can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing.
DOI: 10.1093/bioinformatics/btz198
PubMed: 30903136
Affiliations:
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Le document en format XML
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<front><div type="abstract" xml:lang="en">We set out to develop an algorithm that can mine differential gene expression data to identify candidate cell type-specific DNA regulatory sequences. Differential expression is usually quantified as a continuous score-fold-change, test-statistic, P-value-comparing biological classes. Unlike existing approaches, our de novo strategy, termed SArKS, applies non-parametric kernel smoothing to uncover promoter motif sites that correlate with elevated differential expression scores. SArKS detects motif k-mers by smoothing sequence scores over sequence similarity. A second round of smoothing over spatial proximity reveals multi-motif domains (MMDs). Discovered motif sites can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing.</div>
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