Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data
Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data
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DOI：
10.1186/1471-2105-6-127
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发表时间：
2005-05-27
影响因子：
3
通讯作者：
Liberles, DA
中科院分区：
文献类型：
--
作者：
Rossnes, R;Eidhammer, I;Liberles, DA
背景：在物种形成后，随着基因组的进化，基因含量、编码序列、基因表达和剪接都随着时间的推移而从具有近亲的祖先中分化出来。从系统发育的角度提出了一种用于连续特征分析的最小进化通用方法，该方法允许祖先特征状态的重建和沿分支进化的测量。结果：提供了一个用于重建连续性状的软件包，如相对基因表达水平或替代剪接位点使用数据，可从http://www.rossnes.org/phyrex下载。该程序应用于灵长类基因表达数据集，以检测发生替代的转录因子结合位点，这些位点可能导致基因表达的谱系特异性差异。结论：谱系特异性进化的系统分析正在成为比较基因组学研究的基石。新的方法，如phyrex，通过追踪其他生物分子过程的进化扩展了比较基因组学的能力。
Background: As genomes evolve after speciation, gene content, coding sequence, gene expression, and splicing all diverge with time from ancestors with close relatives. A minimum evolution general method for continuous character analysis in a phylogenetic perspective is presented that allows for reconstruction of ancestral character states and for measuring along branch evolution.Results: A software package for reconstruction of continuous character traits, like relative gene expression levels or alternative splice site usage data is presented and is available for download at http://www.rossnes.org/phyrex. This program was applied to a primate gene expression dataset to detect transcription factor binding sites that have undergone substitution, potentially having driven lineage-specific differences in gene expression.Conclusion: Systematic analysis of lineage-specific evolution is becoming the cornerstone of comparative genomics. New methods, like phyrex, extend the capabilities of comparative genomics by tracing the evolution of additional biomolecular processes.