[1]毕得,肖华军,周翠红,等.心肺细胞缺氧效应生物信息学分析[J].深圳大学学报理工版,2012,29(No.6(471-580)):541-547.[doi:10.3724/SP.J.1249.2012.06541]
 BI De,XIAO Hua-jun,ZHOU Cui-hong,et al.Bioinformatic analysis of ?cardiac and pulmonary hypoxia[J].Journal of Shenzhen University Science and Engineering,2012,29(No.6(471-580)):541-547.[doi:10.3724/SP.J.1249.2012.06541]
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心肺细胞缺氧效应生物信息学分析()
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《深圳大学学报理工版》[ISSN:1000-2618/CN:44-1401/N]

卷:
第29卷
期数:
2012年No.6(471-580)
页码:
541-547
栏目:
生物工程
出版日期:
2012-11-30

文章信息/Info

Title:
Bioinformatic analysis of ?cardiac and pulmonary hypoxia
文章编号:
20120613
作者:
毕得1肖华军13周翠红2邓小燕2温冬青3
1)北京航空航天大学航空科学与工程学院,北京 100191
2)北京航空航天大学生物与医学工程学院,教育部生物力学重点实验室,北京 100191
3)空军航空医学研究所,北京 100142
Author(s):
BI De1 XIAO Hua-jun13 ZHOU Cui-hong2 DENG Xiao-yan2 and WEN Dong-qing3
1) School of Aeronautic Science and Engineering, Beihang University, Beijing 100191, P.R.China
2) Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Biomedical Engineering, Beihang University, Beijing 100191, P.R.China
3) Institute of Aviation Medicine, Beijing 100142, P.R.China
关键词:
生物信息学缺氧BRB-Array工具GEO数据库文本挖掘差异表达基因小分子RNA信号通路生物学过程
Keywords:
bioinformatics hypoxia BRB-ArrayTools GEO database literature mining differential expression gene microRNA (miRNA) signaling pathways biological processes
分类号:
R 318.04
DOI:
10.3724/SP.J.1249.2012.06541
文献标志码:
A
摘要:
采用BRB-ArrayTools分析GEO数据库中肺和心脏细胞在缺氧环境下不同时间段的差异表达基因,获得肺细胞差异表达基因39个,心脏细胞差异表达基因66个,其中,有部分差异表达基因相同,但更多是不同的响应基因;差异表达基因随缺氧时间延长达到相对稳定. 通过GeneCodis聚类这些差异表达基因参与的分子功能和生物学过程,其功能涉及血管生成、NAD+活性、跨膜转运作用、还原酶作用、氧化还原过程及氧化应激等. 用本文挖掘找出缺氧调控的microRNA (miRNA),用miTALOS分析缺氧调控miRNA参与的生物信号通路,这些信号通路主要有血管内皮生长因子(vascular endothelial growth-factor,VEGF)受体功能、Wnt和MAPK (mitogen-activated protein kinase)信号通路. 结果表明,挖掘和整合生物基因芯片有效信息资源,可为深入研究缺氧效应的分子机理提供新思路.
Abstract:
BRB-ArrayTools was used to analyze differentially expressed genes of samples of pulmonary microvascular endothelial cells and cardiac microvascular endothelial cells cultured in hypoxia. 39 and 66 differentially expressed genes were obtained from pulmonary cells and cardiac cells respectively. The differentially expressed genes showed a relatively stable expression trend in response to hypoxia with the increase of hypoxia time. Genecodis analisis showed that the differentially expressed genes were involved in angiogenesis, NAD+activity, transmembrane transport, redox processes, and oxidative stress. Literature mining was applied to obtain the hypoxia-regulated microRNAs (miRNAs) from previously published literature. ?The hypoxia-regulated miRNAs were ?involved in VEGF (vascular endothelial growth-factor) receptor function, Wnt and MAPK (mitogen-activated protein kinase) pathway. The results show that mining bioinformation in gene chip and integrating distributed resources of the ?literature database could deepen understanding of biological processes of genes and miRNAs involved in hypoxia, and these data benefit further investigation and cognitive perspective of the molecular mechanisms of hypoxia.

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备注/Memo

备注/Memo:
Received:2012-07-11;Accepted:2012-11-13
Foundation:National Natural Science Foundation of China (11072023, 31170904)
Corresponding author:Professor XIAO Hua-jun. E-mail: xiao-hj@263.net
Citation:BI De, XIAO Hua-jun, ZHOU Cui-hong, et al. Bioinformatic analysis of ?cardiac and pulmonary hypoxia[J]. Journal of Shenzhen University Science and Engineering, 2012, 29(6): 541-547.(in Chinese)
基金项目:国家自然科学基金资助项目(11072023, 31170904)
作者简介:毕得(1982-),男(汉族),河北省张家口市人,北京航空航天大学博士研究生. E-mail:bdnoxt@gmail.com
引文:毕得,肖华军,周翠红,等. 心肺细胞缺氧效应生物信息学分析[J]. 深圳大学学报理工版,2012,29(6): 541-547.
更新日期/Last Update: 2012-11-30