基因簇谱载体:一种利用基因接近性和共现谱推断功能耦合的新方法

V. Pejaver, Sun Kim
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引用次数: 0

摘要

基于接近的方法和基于共同进化的系统发育谱方法已经成功地用于功能相关基因的鉴定。基于接近度的方法对物理聚类基因有效,而系统发育谱方法对共发生基因集有效。然而,这两种方法都预测了许多假阳性和假阴性。在本文中,我们提出了基因簇特征向量(GCPV)方法,该方法利用整个基因簇的系统发育特征将这两种方法结合起来。此外,GCPV方法是目前唯一允许表征基因簇本身之间关系的方法。GCPV方法在大约60%的时间内将大肠杆菌中合理相关的操纵子组合在一起。该方法对参考基因组集的依赖最小,优于传统的系统发育谱方法。最后,我们证明该方法可以很好地预测月牙菇的基因簇,不仅可以作为理解基因功能的重要工具,而且可以作为阐明一般生物学过程机制的重要工具。
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Gene cluster profile vectors: A novel method to infer functional coupling using both gene proximity and co-occurrence profiles
Proximity-based methods and co-evolution-based phylogenetic profiles methods have been successfully used for the identification of functionally related genes. Proximity-based methods are effective for physically clustered genes while the phylogenetic profiles method is effective for co-occurring gene sets. However, both methods predict many false positives and false negatives. In this paper, we propose the Gene Cluster Profile Vector (GCPV) method, which combines these two methods by using phylogenetic profiles of whole gene clusters. Moreover, the GCPV method is, currently, the only method that allows for the characterization of relationships between gene clusters themselves. The GCPV method groups together reasonably related operons in E. coli about 60% of the time. The method is minimally dependent on the reference genome set used and it outperforms the conventional phylogenetic profiles method. Finally, we show that the method works well for predicted gene clusters from C. crescentus and can serve as an important tool not only for understanding gene function, but also for elucidating mechanisms of general biological processes.
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