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Please use this identifier to cite or link to this item: http://ntour.ntou.edu.tw:8080/ir/handle/987654321/51275

Title: Discovering gapped binding sites of yeast transcription factors
Authors: Chien-Yu Chen
Huai-Kuang Tsai
Chen-Ming Hsu
Mei-Ju May Chen
Hao-Geng Hung
Grace Tzu-Wei Huang
Wen-Hsiung Li
Contributors: 國立臺灣海洋大學:資訊工程學系
Keywords: binding motif
ChIP-chip data
gapped motifs
pattern mining
regulatory elements
Date: 2008
Issue Date: 2018-11-21T07:24:06Z
Publisher: Proc Natl Acad Sci U S A
Abstract: Abstract: A gapped transcription factor-binding site (TFBS) contains one or more highly degenerate positions. Discovering gapped motifs is difficult, because allowing highly degenerate positions in a motif greatly enlarges the search space and complicates the discovery process. Here, we propose a method for discovering TFBSs, especially gapped motifs. We use ChIP-chip data to judge the binding strength of a TF to a putative target promoter and use orthologous sequences from related species to judge the degree of evolutionary conservation of a predicted TFBS. Candidate motifs are constructed by growing compact motif blocks and by concatenating two candidate blocks, allowing 0–15 degenerate positions in between. The resultant patterns are statistically evaluated for their ability to distinguish between target and nontarget genes. Then, a position-based ranking procedure is proposed to enhance the signals of true motifs by collecting position concurrences. Empirical tests on 32 known yeast TFBSs show that the method is highly accurate in identifying gapped motifs, outperforming current methods, and it also works well on ungapped motifs. Predictions on additional 54 TFs successfully discover 11 gapped and 38 ungapped motifs supported by literature. Our method achieves high sensitivity and specificity for predicting experimentally verified TFBSs.
Relation: 105(7) pp.2527-2532
URI: http://ntour.ntou.edu.tw:8080/ir/handle/987654321/51275
Appears in Collections:[資訊工程學系] 期刊論文

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