title: PeakRegressor identifies composite sequence motifs responsible for STAT1 binding sites and their potential rSNPs.
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.
authors.affiliation: Computational Biology Research Center, Advanced Industrial Science and Technology, Tokyo, Japan.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Pessiot
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Chiba
authors.forename: Hiroto
authors.initials: H
authors.lastname: Hyakkoku
authors.forename: Takeaki
authors.initials: T
authors.lastname: Taniguchi
authors.forename: Wataru
authors.initials: W
authors.lastname: Fujibuchi
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology; D016014:Linear Models; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D025341:Principal Component Analysis; D012319:RNA Polymerase II / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D050794:STAT1 Transcription Factor / Q000378:metabolism*
chemical_list: D050794:STAT1 Transcription Factor; D012319:RNA Polymerase II
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