基因组中基因片段组织的图分析
Graph Based Analysis for Gene Segment Organization In a Scrambled Genome
摘要：
DNA重排过程以多种方式重组染色体上的基因片段。段可以重叠、交错或一个可以是另一个的子段。我们使用有向图来表示给定位点上的片段组织，其中包含重排片段的重叠群表示顶点，边缘对应于片段关系。使用图形的属性，我们在一个更高的维欧几里德空间中的一个点相关联的每个图，使集群的形成和分析，可以与拓扑数据分析的方法进行。该方法适用于最近测序的模式生物\textit{Oxytricha trifallax}，一种纤毛虫高度混乱的基因组，经历大规模的重排过程后接合。分析显示了一些新兴的星形图结构，表明单个基因的片段可以交织，甚至在其片段之间包含来自15个或更多其他基因的所有片段。我们还观察到，多达六个基因的片段可以相互交错或重叠。
英文摘要：
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment organizations on a given locus where contigs containing rearranged segments represent vertices and the edges correspond to the segment relationships. Using graph properties we associate a point in a higher dimensional Euclidean space to each graph such that cluster formations and analysis can be performed with methods from topological data analysis. The method is applied to a recently sequenced model organism \textit{Oxytricha trifallax}, a species of ciliate with highly scrambled genome that undergoes massive rearrangement process after conjugation. The analysis shows some emerging star-like graph structures indicating that segments of a single gene can interleave, or even contain all of the segments from fifteen or more other genes in between its segments. We also observe that as many as six genes can have their segments mutually interleaving or overlapping.
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