天津医药

天津医药 ›› 2015, Vol. 43 ›› Issue (6): 616-619.doi: 10.11958/j.issn.0253-9896.2015.06.010

• 实验研究 • 上一篇    下一篇

年龄对骨折愈合影响的生物信息学分析

王顺义，李辉，胡长清，任东良，马伟松，李伟峰，于涛   

  1. 保定市第一中心医院骨一科


  • 收稿日期:2014-10-31 修回日期:2015-01-15 出版日期:2015-06-15 发布日期:2015-06-10
  • 通讯作者: 李辉 E-mail:huili2000hl@163.com

Using bioinformatics to analyze the effect of age on fracture healing

WANG Shunyi, LI Hui, HU Changqing, REN Dongliang, MA Weisong, LI Weifeng, YU Tao   

  1. The First Department of Orthopaedies, Baoding First Central Hospital
  • Received:2014-10-31 Revised:2015-01-15 Published:2015-06-15 Online:2015-06-10

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摘要： 目的 探索年龄对骨折愈合速度的影响， 并寻找在年龄对骨折愈合速度产生影响的过程中起重要作用的基因和通路。方法 利用 R 编程语言， 分别找到在各时间点 （未骨折， 骨折后 3 d、 1 周、 2 周、 4 周和 6 周） 26 周龄大鼠和 52 周龄大鼠相对于 6 周龄大鼠的差异表达基因， 通过比较这 12 组差异表达基因， 找到能够使年龄对骨折愈合产生影响的基因， 利用 DAVID 数据库对这些基因进行功能注释， 并通过 STRING 数据库构建这些基因的 PPI 网络。结果 未骨折、 骨折后 2 周、 4 周、 6 周， 52 周龄大鼠的差异表达基因均多于 26 周龄大鼠； 骨折后 6 周， 26 周龄大鼠只有 4 个差异表达基因， 而 52 周龄大鼠中有 99 个。这 99 个差异表达基因主要富集于与骨骼生长、 免疫和炎症等相关的生物过程， 富集的 KEGG 通路有 2 条： ECM-receptor interaction 和 Arachidonic acid metabolism。Pcna、 Casp3和 Fn1 等在 PPI 网络中与其他基因联系较密切。结论 Pcna、 Casp3 和 Fn1 等基因可能在骨折愈合中起重要作用，其可能通过影响 ECM-receptor interaction 和 Arachidonic acid metabolism 等通路来发挥作用。

关键词: 计算生物学, 骨折, 年龄因素, R 编程语言, 通路, PPI 网络

Abstract: Objective To explore the effect of age on the fracture healing through bioinformatical analysis of gene expression data in GEO, and to screen critical molecular targets and pathways involved in this process. Methods Through R programming language, we identified different expressed genes between 26/52 week old rats and 6 week old rats in every time points of the experiment (No fracture; 3 days, 1 week, 2 weeks, 4 weeks and 6 weeks after fracture). By comparison of
these different expressed genes, those genes that may contribute to fracture healing were identified. Function annotation was conducted based on DAVID database and PPI network that was constructed via STRING database. Results Compared with 6 week old rat, 52 week old rat show more different genes at 2, 4 and 6 weeks after fracture as well as more than intact rats.At the time point of 6 weeks after fracture, 26 week old rat present 4 different genes while 52 week old rat present 99 different genes compared with 6 week old rat. We totally found 99 genes that might play important roles in the process of fracture
healing. These genes involved in biological process related to bone healing, immune, inflammatory and etc. Also, two screened gene enriched KEGG pathways were identified: ECM- receptor interaction and Arachidonic acid metabolism.Through the analysis of PPI network, Pcna, Fn1, Casp3 and etc, who present high density connectivity in PPI network, were screened out. Conclusion Pcna, Casp3 and Fn1 and etc might play important roles in fracture healing through affecting ECM-receptor interaction and Arachidonic acid metabolism.

Key words: computational biology, fracture, age factors, R programming language, pathway, PPI network