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Identify SSR Regulators for Functional Gene Sets through Cross-Species Comparison

机译：通过跨物种比较确定功能基因集的SSR调控子

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摘要

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.
机译：单序列重复（SSR）是由相对较短基序的串联重复组成的DNA序列。它们不仅被视为遗传标记，而且在基因调控网络中发挥重要作用，而基因调控网络是功能基因组学的最大挑战之一。为了在功能基因集中识别关键的SSR调控子，我们开发了一种有效的SSR模式检索算法和基于跨物种比较和统计分析的验证机制。跨物种比较和直系同源关系提供了更高的验证水平，可用于识别可能受到类似调控的多个基因。另外，出现频率的统计分析证实了检索到的SSR是来自给定一组相关基因的重要调控因子。在这项研究中，评估了与生长因子相关基因有关的靶基因，并通过我们提出的系统成功鉴定了几种众所周知的“ CA”，“ CCG”和“ CAG”重复模式。因此，针对所有感兴趣的生物和基因成功地实现了提出的用于分析大规模基因组数据集的新颖模式挖掘方法，并且所提出的机制可以用于检索SSR调控子的重要候选物，以进行进一步的生物学实验。

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  • 来源
    《》|2008年|204-211|共8页
  • 会议地点 Lijiang(CN);Lijiang(CN)
  • 作者

    LI Chen; rnDUAN Chenggang; rnZHOU Aihua;

  • 作者单位

    Chien-Ming Chen@Department of Computer Science and Engineering, National Taiwan Ocean University, No. 2, Pei-Ning Rd., Keelung, Taiwan 20224, China.--Meng-Chang Hsiao@Department of Computer Science and Engineering, National Taiwan Ocean University, No. 2, Pei-Ning Rd., Keelung, Taiwan 20224, China.--Tun-Wen Pai@Department of Computer Science and Engineering, National Taiwan Ocean University, No. 2, Pei-Ning Rd., Keelung, Taiwan 20224, China.--Ronshan Cheng@Department of Aquaculture, National Taiwan Ocean University, No. 2, Pei-Ning Rd., Keelung, Taiwan 20224, China.--Wen-Shyong Tzou@Institute of Bioscience and Biotechnology, National Taiwan Ocean University,No. 2, Pei-Ning Rd., Keelung, Taiwan 20224, China.--Margaret Dah-Tsyr Chang@Institute of Molecular and Cellular Biology Department o;

  • 会议组织
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 生物工程学（生物技术）;
  • 关键词

    simple sequence repeat; microsatellite; functional significance score (FSS); orthologous conservation score (OCS); gene regulatory networks; regulator;

    机译：简单重复序列;微卫星;功能重要性评分（​​FSS）;直系保守评分（OCS）;基因调控网络;调控子;

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