基于最大信息系数的永久性房颤差异表达基因识别

doi:103969/j.issn.0258-8021.2015.01.002

摘要
图/表
参考文献
相关文章 (0)

全文: PDF (843 KB) HTML (1 KB)
输出: BibTeX | EndNote (RIS)

摘要心房颤动是一种常见的、与年龄相关的心律失常，由其所导致的脑卒中具有高致残率和致死率。通过对高通量基因表达谱的分析，可以帮助理解心房颤动的生物学过程和功能紊乱机制，并发现相关致病基因。新型的非参数统计方法——最大信息系数，在探索双变量之间的关联方面具有独特的优点。利用该方法，发现差异与非差异基因表达值与样本表型之间的关联程度不同，构建差异表达基因识别方法。对永久性房颤基因表达谱GSE2240的分析，识别出41个差异表达基因，其中有14基因是已有工作未发现的新差异表达基因。信号通路和富集分析表明，这些差异表达基因与房颤高度相关。同时，对乳腺癌基因表达数据GSE24037的分析，进一步说明该方法在差异表达基因识别方面的有效性。最大信息系数的非参数特性与抗噪能力，使它非常适合于差异表达基因的识别。

	服务

	把本文推荐给朋友
	加入我的书架
	加入引用管理器
	E-mail Alert
	RSS
	作者相关文章
	刘汉明¹
	2 饶妮妮^1*李益¹罗恒荣¹杨阳¹

关键词 ：最大信息系数, 心房颤动, 差异表达基因

Abstract：The atrial fibrillation is a common arrhythmia disease. It usually causes stroke resulting in high risk on morbidity and mortality. It can be insight into the biological processes, the functional disorders of atrial fibrillation and the genes associated with disease risks by analyzing a microarray data. A proposed novel statistical method named as maximal information coefficient (MIC) has excellent performance in exploring the relationship between twovariables. Based on the degree of relationship between the phenotypes and differentially or undifferentially expressed genes, the statistical method was introduced into the analysis of a microarray of permanent atrial fibrillations (GSE2240). Total of 41 genes were identified by the method, in which 14 genes are new differentially expressed genes. The differentially expressed genes identified by MIC were demonstrated that they were related with atrial fibrillation diseases, via the analyses of signaling pathway and enrichment in DAVID. Furthermore, MIC was used to analyze a microarray of breast cancer (GSE24037) to test the method. MIC is a nonparametric statistical method with antinoise, which leads it to be ideally suit for identifying differentially expressed genes.

Key words： maximal information coefficient atrial fibrillation differentially expressed gene

基金资助:国家自然科学基金（81171411）

引用本文:

刘汉明^1,2饶妮妮^1*李益¹罗恒荣¹杨阳^{1 Liu Hanming^1,2Rao Nini^1*Li Yi¹Luo Hengrong¹Yang Yang¹Yang Feng¹. Maximal Information Coefficient on Identifying Differentially Expressed Genes of Permanent Atrial Fibrillation. journal1, 2015, 34(1): 8-16.}

链接本文:

http://cjbme.csbme.org/CN/103969/j.issn.0258-8021.2015.01.002 或 http://cjbme.csbme.org/CN/Y2015/V34/I1/8

［1］Schotten U, Ausma J, Stellbrink C, et al. Cellular mechanisms of depressed atrial contractility in patients with chronic atrial fibrillation［J］. Circulation, 2001, 103(5):691698.
［2］Nattel S. New ideas about atrial fibrillation 50 years［J］. Nature, 2002, 415(6868):219-226.
［3］涂承媛, 曾衍钧, 李树信. 房颤心电信号的分形维分析［J］. 中国生物医学工程学报, 2005, 24(2):163-166.
［4］刘靖. 心房颤动的治疗进展［J］. 西部医学, 2013, 25(10):1593-1595. 
［5］Benjamin EJ, Wolf PA, D’Agostino RB, et al. Impact of atrial fibrillation on the risk of death the Framingham Heart Study［J］. Circulation, 1998, 98(10):946-952.
［6］Ho KK, Pinsky JL, Kannel WB, et al. The epidemiology of heart failure: the Framingham Study［J］. Journal of the American College of Cardiology, 1993, 22(4s1):A6-A13.
［7］Wolf PA, Abbott RD, Kannel WB. Atrial fibrillation as an independent risk factor for stroke: the Framingham study［J］. Stroke, 1991, 22(8):983-988.
［8］李靖, 陈宇光, 孔祥银. 基因表达系列分析技术的新进展［J］. 生物工程学报, 2001, 17(6):613-616.
［9］Kim YH, Lee JH, Lim DS, et al. Gene expression profiling of oxidative stress on atrial fibrillation in humans［J］. Experimental and Molecular Medicine, 2003, 35(5):336-349.
［10］Ohki-Kaneda R, Ohashi J, Yamamoto K, et al. Cardiac functionrelated gene expression profiles in human atrial myocytes［J］. Biochemical and Biophysical Research Communications, 2004, 320(4):1328-1336.
［11］Barth AS, Merk S, Arnoldi E, et al. Reprogramming of the human atrial transcriptome in permanent atrial fibrillation expression of a ventricularlike genomic signature［J］. Circulation Research, 2005, 96(9):1022-1029.
［12］Censi F, Calcagnini G, Bartolini P, et al. A systems biology strategy on differential gene expression data discloses some biological features of atrial fibrillation［J］. PLoS One, 2010, 5(10):e13668.
［13］Reshef DN, Reshef YA, Finucane HK, et al. Detecting novel associations in large data sets［J］. Science, 2011, 334(6062):1518-1524.
［14］Jiao Xiaoli, Sherman BT, Huang DaWei, et al. DAVIDWS: a stateful web service to facilitate gene/protein list analysis［J］. Bioinformatics, 2012, 28(13):1805-1806.［15］Furlanello C, Serafini M, Merler S, et al. Entropybased gene ranking without selection bias for the predictive classification of microarray data［J］. BMC bioinformatics, 2003, 4(1):54-73.
［16］Huang DaWei, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists［J］. Nucleic Acids Research, 2009, 37(1):1-13.
［17］Nishimura D. BioCarta［J］. Biotech Software & Internet Report: The Computer Software Journal for Scient, 2001, 2(3):117-120.
［18］刘明, 王米渠, 丁维俊, 等. 表达谱芯片数据的基因功能富集分析［J］. 生物医学工程学杂志, 2010, 27(5):1166-1169. 
［19］尤元海, 张建中. 基因表达谱芯片的数据挖掘［J］. 中国生物工程杂志, 2009, 29(10):87-91.
［20］蒋定锋, 潘娟娟, 赵耐青. 差异表达基因筛选方法的比较［J］. 中国卫生统计, 2006, 23(5):417-420.
［21］李运明, 曹文君, 陈长生. 六种基因表达谱数据筛选差异表达基因方法的比较［J］. 中国卫生统计, 2009,(3):250-254.
［22］Shi Yigong, Massagué J. Mechanisms of TGF β signaling from cell membrane to the nucleus［J］. Cell, 2003, 113(6):685-700.
［23］Camm AJ, Kirchhof P, Lip GY, et al. Guidelines for the management of atrial fibrillation: The Task Force for the Management of Atrial Fibrillation of the European Society of Cardiology (ESC)［J］. European Heart Journal, 2010, 31(19):2369-2429.
［24］Burstein B, Nattel S. Atrial fibrosis: mechanisms and clinical relevance in atrial fibrillation［J］. Journal of the American College of Cardiology, 2008, 51(8):802-809.
［25］Patterson GI, Padgett RW. TGFβrelated pathways: roles in Caenorhabditis elegans development［J］. Trends in Genetics, 2000, 16(1):27-33.
［26］Dijke PT, Goumans MJ, Itoh F, et al. Regulation of cell proliferation by Smad proteins［J］. Journal of Cellular Physiology, 2002, 191(1):1-16.
［27］Massagué J. How cells read TGFβ signals［J］. Nature Reviews Molecular Cell Biology, 2000, 1(3):169-178.
［28］RuizOrtega M, RodríguezVita J, SanchezLopez E, et al. TGFβ signaling in vascular fibrosis［J］. Cardiovascular Research, 2007, 74(2):196-206.
［29］ClarkGreuel JN, Connolly JM, Sorichillo E, et al. Transforming growth factorβ1 mechanisms in aortic valve calcification: increased alkaline phosphatase and related events［J］. The Annals of Thoracic Surgery, 2007, 83(3):946-953.
［30］Shiomi T, Tsutsui H, Hayashidani S, et al. Pioglitazone, a peroxisome proliferatoractivated receptorγ agonist, attenuates left ventricular remodeling and failure after eperimental myocardial infarction［J］. Circulation, 2002, 106(24):3126-3132.
［31］Everett TH, Olgin JE. Atrial fibrosis and the mechanisms of atrial fibrillation［J］. Heart Rhythm, 2007, 4(3):S24-S27.
［32］马宁, 张正国. 一种基于 Gene Ontology 注释信息的基因选择算法［J］. 中国生物医学工程学报, 2009, 28(5):696-700.
［33］Goette A, Staack T, Rcken C, et al. Increased expression of extracellular signalregulated kinase and angiotensinconverting enzyme in human atria during atrial fibrillation［J］. Journal of the American College of Cardiology, 2000, 35(6):1669-1677.
［34］Xu Jun, Cui Guanggen, Esmailian F, et al. Atrial extracellular matrix remodeling and the maintenance of atrial fibrillation［J］. Circulation, 2004, 109(3):363-368.
［35］VanWagoner DR , Pond AL, McCarthy PM, et al. Outward K+ current densities and Kv1 5 expression are reduced in chronic human atrial fibrillation［J］. Circulation Research, 1997, 〖STHZ〗80〖STBZ〗(6):772-781.
［36］AiméSempé C, Folliguet T, RückerMartin C, et al. Myocardial cell death in fibrillating and dilated human right atria［J］. Journal of the American College of Cardiology, 1999, 34(5):1577-1586.
［37］Li Duosheng, Cardin S, Han Hao, et al. Signal transduction underlying arrhythmogenic atrial remodeling due to congestive heart failure［C］ // McCann J, eds. Circulation Conference 2000. Philadelphia: Lippincott Williams & Wilkins, 2000: 153-153.
［38］Goette A, Arndt M, Rcken C, et al. Regulation of angiotensin II receptor subtypes during atrial fibrillation in humans［J］. Circulation, 2000, 101(23):2678-2681.
［39］Lendeckel U, Arndt M, Wrenger S, et al. Expression and activity of ectopeptidases in fibrillating human atria［J］. Journal of Molecular and Cellular Cardiology, 2001, 33(6):1273-1281.
［40］Tuinenburg AE, VanVeldhuisen DJ , Boomsma F , et al. Comparison of plasma neurohormones in congestive heart failure patients with atrial fibrillation versus patients with sinus rhythm［J］. The American Journal of Cardiology, 1998, 81(10):1207-1210.
［41］Goette A, Lendeckel U, Klein HU. Signal transduction systems and atrial fibrillation［J］. Cardiovascular Research, 2002, 54(2):247-258.
［42］Li Maomi, Vuolo MA, Weidenheim KM, et al. Collectingduct carcinoma of the kidney with prominent signet ring cell features［J］. Modern Pathology, 2001, 14(6):623-628.