[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]
点击复制

心肺细胞缺氧效应生物信息学分析()
分享到：

《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1; 3; 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-jun1; 3;  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.

参考文献/References:

［1］ Chaiban J T, Bitar F F, Azar S T. Effect of chronic hypoxia on leptin, insulin, adiponectin, and ghrelin［J］. Metabolism, 2008, 57(8): 1019-1022.
［2］ BAO Huan, BAO Shi-yao. Molecular mechanisms of blood-brain barrier tight junction change after hypoxia［J］. Cerebrovascular Diseases Foreign Medical Sciences, 2005, 13(8): 604-608.(in Chinese)
鲍欢, 包仕尧. 缺氧后血脑屏障紧密连接变化的分子机制［J］. 国外医学脑血管疾病分册, 2005, 13(8): 604-608.
［3］ Howell K, Ooi H, Preston R, et al. Structural basis of hypoxic pulmonary hypertension: the modifying effect of chronic hypercapnia ［J］. Experimental Physiology, 2004, 89(1): 66-72.
［4］ Pierson D J. Pathophysiology and clinical effects of chronic hypoxia［J］. Respir Care, 2000, 45(1): 39-53.
［5］ Busl K M, Greer D M. Hypoxic-ischemic brain injury: pathophysiology, neuropathology and mechanisms［J］. Neuro Rehabilitation, 2010, 26(1): 5-13.
［6］ Thiersch M, Raffelsberger W, Frigg R, et al. Analysis of the retinal gene expression profile after hypoxic preconditioning identifies candidate genes for neuroprotection［J］. BMC Genomics, 2008, 9: 73.
［7］ JIANG Chun-hua，HUANG Qing-yuan, GAO Yu-qi，et al. Hypoxic preconditioning improves the brain function of recruits after ascending to high altitude by air ［J］. Journal of Preventive Medicine of Chinese People’s Liberation Army, 2005, 23(5): 323-326.(in Chinese)
蒋春华, 黄庆愿, 高钰琪, 等. 预适应锻炼对急进高原新兵脑功能的保护作用［J］. 解放军预防医学杂志, 2005, 23(5): 323-326.
［8］ Costello C M, Howell K, Cahill E, et al. Lung-selective gene responses to alveolar hypoxia: potential role for the bone morphogenetic antagonist gremlin in pulmonary hypertension［J］. American Journal of Physiology-Lung Cellular and Molecular Physiology, 2008, 295(2): L272-284.
［9］ Zhao Y, Simon R. BRB-ArrayTools Data Archive for human cancer gene expression: a unique and efficient data sharing resource［J］. Cancer Inform, 2008, 6 9-15.
［10］ Nogales-Cadenas R, Carmona-Saez P, Vazquez M, et al. GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information［J］. Nucleic Acids Research, 2009, 37(web server issue): W317-W322.
［11］ Kowarsch A, Preusse M, Marr C, et al. miTALOS: analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs［J］. RNA, 2011, 17(5): 809-819.
［12］ Kanehisa M, Goto S, Furumichi M, et al. KEGG for representation and analysis of molecular networks involving diseases and drugs［J］. Nucleic Acids Research, 2010, 38(database issue): D355-D360.
［13］ XIA Li-xin,YAN Hao,TANG Mu-jin, et al. Bioinformatics comparison of peanut allergen Ara h2 and Ara h6［J］. Journal of Shenzhen University Science and Engineering, 2010, 27(2): 241-246.(in Chinese)
夏立新, 闰浩, 汤慕瑾, 等. 花生过敏原Ara h2 与Ara h6 的生物信息学比较研究［J］. 深圳大学学报理工版, 2010, 27(2): 241-246.
［14］ WANG Xiao-dong,JIANG Yong, CHEN Min-sheng. Proteomics analysis on rats soleus muscle fibers following hindlimb suspension［J］. Journal of Shenzhen University Science and Engineering, 2010, 27(4): 502-504.(in Chinese)
王晓东, 姜咏, 陈民盛. 后肢悬吊后大鼠比目鱼肌的蛋白质组学解析［J］. 深圳大学学报理工版, 2010, 27(4): 502-504.
［15］ Taie S, Ono J, Iwanaga Y, et al. Hypoxia-inducible factor-1 alpha has a key role in hypoxic preconditioning［J］. Journal of Clinical Neuroscience, 2009, 16(8): 1056-1060.
［16］ ZHOU Jian-guang, FANG Yi-qun, LIU Chang-yun, et al.Effect of hyperbaric oxygen on the expression of nitric oxide synthase mRNA in cortex after acute traumatic cerebral injury［J］. Chinese Journal of Applied Physiology, 2012, 28(1): 38-41.(in Chinese)
周建光, 方以群, 刘长云, 等. 高压氧对急性脑创伤后皮层一氧化氮合酶mRNA表达的影响［J］. 中国应用生理学杂志, 2012, 28(1): 38-41.
［17］ JIANG Li-hua, DU Li-zhong.Expressions of NOX4 and eNOS in pulmonary vasculature in mouse model of chronic hypoxia［J］. Journal of Clinical Pulmonary Medicine, 2011, 16(5): 679-681.(in Chinese)
姜丽华, 杜立中. NOX4和eNOS在小鼠慢性缺氧肺血管重塑中的表达及意义［J］. 临床肺科杂志, 2011, 16(5): 679-681.
［18］ Aggarwal S, Negi S, Jha P, et al. EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda［J］. Proceedings of the National Academy of Sciences, 2010, 107(44): 18961-18966.
［19］ XU Fei-fei, LIU Xiu-hua, CAI Li-rong. Role of hypoxia-inducible factor-1α in the prevention of cardiomyocyte injury induced by hypoxic preconditioning［J］. Acta Physiological Sinica, 2004, 56(5): 609-614.(in Chinese)
徐菲菲, 刘秀华, 蔡莉蓉. 缺氧诱导因子-1α 在缺氧预处理预防心肌细胞损伤中的作用［J］. 生理学报, 2004, 56(5): 609-614.
［20］ LI Yu-yu, ?XU Jian-wen, GUO Wei, et al. Effects of transient hypoxia on apoptosis and neurogenesis in the newborn rat brain［J］. Acta Anatomica Sinica, 2011, 42(6): 741-745.(in Chinese)
李玉宇, 徐剑文, 郭玮, 等. 短暂缺氧对新生鼠脑细胞凋亡和神经再生的影响［J］. 解剖学报, 2011, 42(6): 741-745.
［21］ WU Tian-yi. The beneficial effects of plateau environmen on human［J］. Journal of Medical Research, 2007, 36(12): 1-3.(in Chinese)
吴天一. 高原环境对人体有益影响的研究［J］. 医学研究杂, 2007, 36(12): 1-3.
［22］ Bushati N, Cohen S M. microRNA functions［J］. Annual Review of Cell Developmental Biology, 2007, 23 175-205.
［23］ FAN You-ming, GAO Yu-qi, LIU Fu-yu, et al. Protective roles of hypobaric hypoxic pretreatment on hippocampus neurons in mice［J］. Chinese Journal of Pathophysiology, 2006, 22(1): 93-97.(in Chinese)
范有明, 高钰琪, 刘福玉, 等. 低压缺氧延迟预适应对小鼠海马神经元的保护作用研究［J］. 中国病理生理杂志, 2006, 22(1): 93-97.

相似文献/References:

[1]夏立新,闫浩,汤慕瑾,等.花生过敏原Ara h2与Ara h6的生物信息学比较研究[J].深圳大学学报理工版,2010,27(2):241.
　XIA Li-xin,YAN Hao,TANG Mu-jin,et al.Bioinformatics comparison of peanut allergen Ara h2 and Ara h6[J].Journal of Shenzhen University Science and Engineering,2010,27(No.6(471-580)):241.
[2]唐玉林,曹雁,欧忠华,等.非生物胁迫因子对大豆Sali3-2基因的调控作用[J].深圳大学学报理工版,2012,29(No.1(001-094)):73.[doi:10.3724/SP.J.1249.2012.01073]
　TANG Yu-lin,CAO Yan,OU Zhong-hua,et al.Regulatable gene expression controlled by the promoter of Sali3-2 under different abiotic stresses[J].Journal of Shenzhen University Science and Engineering,2012,29(No.6(471-580)):73.[doi:10.3724/SP.J.1249.2012.01073]
[3]陈梦竹,王秀杰,夏立新.肺腺癌和肺鳞癌中mRNA可变剪接特征的比较[J].深圳大学学报理工版,2017,34(1):33.[doi:10.3724/SP.J.1249.2017.01033]
　Chen Mengzhu,Wang Xiujie,and Xia Lixin.Comparison of alternative splicing in lung adenocarcinoma and lung squamous carcinoma[J].Journal of Shenzhen University Science and Engineering,2017,34(No.6(471-580)):33.[doi:10.3724/SP.J.1249.2017.01033]
[4]娄素琳,朱秀兰,曾志勇,等.盐藻microRNA高通量测序和生物信息学分析[J].深圳大学学报理工版,2018,35(4):331.[doi:10.3724/SP.J.1249.2018.04331]
　LOU Sulin,ZHU Xiulan,ZENG Zhiyong,et al.Bioinformatics analysis of Dunaliella microRNAs by high-throughput sequencing[J].Journal of Shenzhen University Science and Engineering,2018,35(No.6(471-580)):331.[doi:10.3724/SP.J.1249.2018.04331]
[5]张尉欣,刘阳,刘 帅,等.镉胁迫下菜心的转录组分析[J].深圳大学学报理工版,2018,35(5):543.[doi:10.3724/SP.J.1249.2018.05543]
　ZHANG Weixin,LIU Yang,LIU Shuai,et al.Transcriptome analysis of Brassica rapa ssp. chinensis var. parachinensis under cadmium stress[J].Journal of Shenzhen University Science and Engineering,2018,35(No.6(471-580)):543.[doi:10.3724/SP.J.1249.2018.05543]
[6]钟姗,等.食管鳞癌中3个新miRNA的分子功能预测[J].深圳大学学报理工版,2019,36(4):347.[doi:10.3724/SP.J.1249.2019.04347]
　ZHONG Shan,WANG Yun,et al.The prediction of molecular functions for three novel miRNAs in esophageal squamous cell carcinoma[J].Journal of Shenzhen University Science and Engineering,2019,36(No.6(471-580)):347.[doi:10.3724/SP.J.1249.2019.04347]
[7]须周恒,朱营利,孙孟菲,等.小鼠纹状体与视网膜的比较转录组学分析[J].深圳大学学报理工版,2020,37(1):17.[doi:10.3724/SP.J.1249.2020.01017]
　XU Zhouheng,ZHU Yingli,SUN Mengfei,et al.Comparative transcriptomic analysis of mouse striatum and retina[J].Journal of Shenzhen University Science and Engineering,2020,37(No.6(471-580)):17.[doi:10.3724/SP.J.1249.2020.01017]
[8]陈扬,陈献雄,欧阳春艳,等.粉尘螨过敏原Der f 35的克隆表达及免疫学鉴定[J].深圳大学学报理工版,2021,38(3):301.[doi:10.3724/SP.J.1249.2021.03301]
　CHEN Yang,CHEN Xianxiong,OUYANG Chunyan,et al.Cloning,expression and immunological identification of Der f 35 allergen from Dermatophagoides farinae[J].Journal of Shenzhen University Science and Engineering,2021,38(No.6(471-580)):301.[doi:10.3724/SP.J.1249.2021.03301]
[9]杨雷,王筠,邓芳,等.糖尿病鼠骨骼肌萎缩相关环状RNA的研究[J].深圳大学学报理工版,2022,39(3):262.[doi:10.3724/SP.J.1249.2022.03262]
　YANG Lei,WANG Yun,DENG Fang,et al.Circular RNAs related to skeletal muscle atrophy in diabetic mouse model[J].Journal of Shenzhen University Science and Engineering,2022,39(No.6(471-580)):262.[doi:10.3724/SP.J.1249.2022.03262]
[10]周彦,江竞舟.COVID-19与SSc-ILD相关性研究[J].深圳大学学报理工版,2023,40(2):171.[doi:10.3724/SP.J.1249.2023.02171]
　ZHOU Yan and JIANG Jingzhou,Association studies between COVID-19 and SSc-ILD[J].Journal of Shenzhen University Science and Engineering,2023,40(No.6(471-580)):171.[doi:10.3724/SP.J.1249.2023.02171]

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