Phylostratigraphic analysis of gene co-expression network reveals the evolution of functional modules for ovarian cancer
Phylostratigraphic analysis of gene co-expression network reveals the evolution of functional modules for ovarian cancer
复制标题
基因共表达网络的系统地层学分析揭示了卵巢癌功能模块的进化
DOI：
10.1038/s41598-019-40023-9
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发表时间：
2019-02-22
影响因子：
4.6
通讯作者：
Zhang，Zhen
中科院分区：
文献类型：
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作者：
Zhang，Luoyan;Tan，Yi;Zhang，Zhen
卵巢癌（OV）是一种极其致命的疾病。然而，OV 的进化机制仍然很大程度上未知。在这里，我们采用了将系统地层学信息与基因共表达网络相结合的方法来广泛研究OV的进化组成。基于从基因组数据分析中心数据库获得的 307 个 OV 表达样本，当前的共表达网络构建产生了 18,549 个节点和 114,985 个边。共有 20 个模块被识别为 OV 相关集群。人类基因组序列分为19个叶层（PS），大多数（67.45%）OV基因已经存在于真核祖先中。超几何检验筛选出OV基因的出现有两个强峰：多细胞后生动物的进化（PS5和PS6，P值= 0.002）和硬骨鱼的出现（PS11和PS12，P值= 0.009）。由此可见，OV的起源远早于它的出现。对OV模块的拓扑结构和系统发育数据的综合分析揭示了人类OV的进化模式，即OV模块在各个谱系的进化过程中逐步出现。新的基因已经进化并被锁定在一条通路中，越来越多的生物通路通过在人类进化过程中招募新基因而被固定到 OV 模块中。
Ovarian cancer (OV) is an extremely lethal disease. However, the evolutionary machineries of OV are still largely unknown. Here, we used a method that combines phylostratigraphy information with gene co-expression networks to extensively study the evolutionary compositions of OV. The present co-expression network construction yielded 18,549 nodes and 114,985 edges based on 307 OV expression samples obtained from the Genome Data Analysis Centers database. A total of 20 modules were identified as OV related clusters. The human genome sequences were divided into 19 phylostrata (PS), the majority (67.45%) of OV genes was already present in the eukaryotic ancestor. There were two strong peaks of the emergence of OV genes screened by hypergeometric test: the evolution of the multicellular metazoan organisms (PS5 and PS6,P value= 0.002) and the emergence of bony fish (PS11 and PS12,P value= 0.009). Hence, the origin of OV is far earlier than its emergence. The integrated analysis of the topology of OV modules and the phylogenetic data revealed an evolutionary pattern of OV in human, namely, OV modules have arisen step by step during the evolution of the respective lineages. New genes have evolved and become locked into a pathway, where more and more biological pathways are fixed into OV modules by recruiting new genes during human evolution.