ArticlePloS one2010
PeakRegressor identifies composite sequence motifs responsible for STAT1 binding sites and their potential rSNPs.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1 citing paper in PubMed.
- Discriminative motif analysis of high-throughput dataset.Bioinformatics (Oxford, England) · 2014Article
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5 authors.
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Abstract
How to identify true transcription factor binding sites on the basis of sequence motif information (e.g., motif pattern, location, combination, etc.) is an important question in bioinformatics. We present "PeakRegressor," a system that identifies binding motifs by combining DNA-sequence data and ChIP-Seq data. PeakRegressor uses L1-norm log linear regression in order to predict peak values from binding motif candidates. Our approach successfully predicts the peak values of STAT1 and RNA Polymerase II with correlation coefficients as high as 0.65 and 0.66, respectively. Using PeakRegressor, we could identify composite motifs for STAT1, as well as potential regulatory SNPs (rSNPs) involved in the regulation of transcription levels of neighboring genes. In addition, we show that among five regression methods, L1-norm log linear regression achieves the best performance with respect to binding motif identification, biological interpretability and computational efficiency.
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