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论文题目: MOST plus : A de novo motif finding approach combining genomic sequence and heterogeneous genome-wide signatures
英文论文题目: MOST plus : A de novo motif finding approach combining genomic sequence and heterogeneous genome-wide signatures
第一作者: Zhang, YZ; He, YP; Zheng, GY; Wei, CC
英文第一作者: Zhang, YZ; He, YP; Zheng, GY; Wei, CC
联系作者: Wei, CC (reprint author), Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, 800 Dongchuan Rd, Shanghai 200240, Peoples R China.
英文联系作者: Wei, CC (reprint author), Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, 800 Dongchuan Rd, Shanghai 200240, Peoples R China.
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发表年度: 2015
卷: 16
期:
页码: -
摘要: Background: Motifs are regulatory elements that will activate or inhibit the expression of related genes when proteins (such as transcription factors, TFs) bind to them. Therefore, motif finding is important to understand the mechanisms of gene regulation. De novo discovery of regulatory elements, like transcription factor binding sites (TFBSs), has long been a major challenge to gain insight on mechanisms of gene regulation. Recent advances in experimental profiling of genome-wide signals such as histone modifications and DNase I hypersensitivity sites allow scientists to develop better computational methods to enhance motif discovery. However, existing methods for motif finding suffer from high false positive rates and slow speed, and it's difficult to evaluate the performance of these methods systematically. Result: Here we present MOST+, a motif finder integrating genomic sequences and genome-wide signals such as intensity and shape features from histone modification marks and DNase I hypersensitivity sites, to improve the prediction accuracy. MOST+ can detect motifs from a large input sequence of about 100 Mbs within a few minutes. Systematic comparison method has been established and MOST+ has been compared with existing methods. Conclusion: MOST+ is a fast and accurate de novo method for motif finding by integrating genomic sequence and experimental signals as clues.
英文摘要: Background: Motifs are regulatory elements that will activate or inhibit the expression of related genes when proteins (such as transcription factors, TFs) bind to them. Therefore, motif finding is important to understand the mechanisms of gene regulation. De novo discovery of regulatory elements, like transcription factor binding sites (TFBSs), has long been a major challenge to gain insight on mechanisms of gene regulation. Recent advances in experimental profiling of genome-wide signals such as histone modifications and DNase I hypersensitivity sites allow scientists to develop better computational methods to enhance motif discovery. However, existing methods for motif finding suffer from high false positive rates and slow speed, and it's difficult to evaluate the performance of these methods systematically. Result: Here we present MOST+, a motif finder integrating genomic sequences and genome-wide signals such as intensity and shape features from histone modification marks and DNase I hypersensitivity sites, to improve the prediction accuracy. MOST+ can detect motifs from a large input sequence of about 100 Mbs within a few minutes. Systematic comparison method has been established and MOST+ has been compared with existing methods. Conclusion: MOST+ is a fast and accurate de novo method for motif finding by integrating genomic sequence and experimental signals as clues.
刊物名称: BMC GENOMICS
英文刊物名称: BMC GENOMICS
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学科: Biotechnology & Applied Microbiology; Genetics & Heredity
英文学科: Biotechnology & Applied Microbiology; Genetics & Heredity
影响因子: 3.986
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论文类别: Article
英文论文类别: Article
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