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Please use this identifier to cite or link to this item: http://ntour.ntou.edu.tw:8080/ir/handle/987654321/27842

Title: Identify SSR Regulators for Functional Gene Sets through Cross-Species Comparison
Authors: Chien-Ming Chen;Meng-Chang Hsiao;Tun-Wen Pai;Ronshan Cheng;Wen-Shyong Tzou;Margaret Dah-Tsyr Chang
Contributors: NTOU:Department of Computer Science and Engineering
國立臺灣海洋大學:資訊工程學系
Keywords: simple sequence repeat;microsatellite;functional significance score (FSS);orthologous conservation score (OCS);gene regulatory networks;regulator
Date: 2008
Issue Date: 2011-10-21T02:34:12Z
Publisher: The Second International Symposium on Optimization and Systems Biology (OSB’08)
Abstract: Abstract:Single sequence repeats (SSRs) are DNA sequences composed of tandem repetitions of relatively short motifs. They are not only considered as genetic markers but also play an important role in gene regulatory networks, One of the greatest challenges of functional genomics. In order to identify key SSR regulators among functional gene sets, we have developed an efficient algorithm for SSR pattern retrieval and a verification mechanism based on cross-species comparison and statistical analysis. Cross-species comparison and orthologous relationship provide an added level of validation for identifying multiple genes that are likely to be regulated similarly. In addition, statistical analysis of appearance frequency rates confirms the retrieved SSRs as significant regulators from a given set of related genes. In this study, the target gene set with growth factor related genes was evaluated and several well known “CA”, “CCG” and “CAG” repeat pattern were successfully identified by our proposed system. Accordingly, the novel pattern mining methods proposed to analyze large-scale genome datasets are successfully achieved for all organisms and genes of interest, and the proposed mechanism can be applied to retrieve important candidates of SSR regulators for further biological experiments.
Relation: pp.204-211
URI: http://ntour.ntou.edu.tw/handle/987654321/27842
Appears in Collections:[資訊工程學系] 演講及研討會

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