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《Hereditas》 2008-09
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Association between ion channel subtype and its gene co-expression

YANG De-Wu1, LI Xia1,2, XIAO Xue1, YANG Yue-Ying1, WANG Jing1 1. Department of Biological Engineering, Capital Medical University, Beijing 100069, China; 2. Department of Bioinformatics, Harbin Medical University, Harbin 150081, China  
Association between ion channel functional subtype and its genes expression is important for exploring function of ion channel, annotating function of an unknown subtype and probing into molecular mechanism of ion channel diseases. In this study, we began with noise reduction by standardizing original micro-array data, which consisted of human and mouse gene expression profiles, and then we employed principle component analysis (PCA) together with fuzzy C-mean clustering algorithm to analyze the pre-processed gene expression profiles. PCA is applied to rebuild the feature space of human gene in 21 dimensions as well as the feature space of mouse gene in 26 dimensions. Using this method we largely reduced computational complexity without losing much information involved in the original data. Subsequently, fuzzy C-mean clustering was used to classify the ion channel genes of human and mouse in their reduced feature space. In the end, four ion channel functional subtypes, such as potassium ion channels, calcium ion channel, chloride ion channel, and recep-tor-mediated ion channel were clustered in both human and mouse gene feature space. We applied two statistic ways to conduct significance test of the findings. In one way, we randomly sampled the data for each functional subtype of the ion channel genes and recorded the true positive rate. As a result, in both human and mouse gene feature spaces, genes thatbelong to one functional subtype were more likely to be clustered together than expected by chance. In the other way, we performed Kappa test and used the functional subtypes as gold standard. The result showed that consistency between the ion channel gene clusters and the ion channel gene subtypes was significantly high for both human and mouse. These results indicate that ion channel genes within the same functional subtype tend to be co-expressed at least at the mRNA-level.
【Fund】: 国家自然科学基金(编号:30571034 30370798);; 国家高技术研究发展计划项目(863 项目) (编号:2007AA02Z329);; 2006年北京市新世纪百千万人才工程 北京市教育委员会科技发展计划项目(编号:KM200610025011)资助~~
【CateGory Index】: Q3
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【Citations】
Chinese Journal Full-text Database 2 Hits
1 GONG Gai-yun~1,MAO Yong-cai~2,GAO Xin-bo~2,LIU San-yang~1 (1.School of Science, Xidian Univ., Xi′an710071, China; 2. School of Electronic Engineering, Xidian Univ., Xi′an710071, China);Fuzzy c-mean clustering method for analyzing microarray gene expression data[J];西安电子科技大学学报;2004-02
2 YANG Chang, FANG Fu-De*(National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences,CAMS and PUMC, Beijing 100005, China);Data analysis in microarray experiment[J];生命科学;2004-01
【Co-citations】
Chinese Journal Full-text Database 10 Hits
1 WANG Wen-Jun (School of Computer Science and Technology,Xidian University,Xi'an 710071);Clustering Analysis of Gene Expression Data Based on Transitive Co-Expression[J];模式识别与人工智能;2012-06
2 YU Zhe(College of Life Sciences,Zhejiang University,Hangzhou 310058,China);Genechip Techonology and Its Data Analysis[J];科技通报;2012-05
3 QIN Chuandong1,LIU Sanyang2,ZHANG Shifang1(1.School of Computer Science and Technology,Xidian Univ.,Xi'an 710071,China; 2.School of Science,Xidian Univ.,Xi'an 710071,China);Method for extracting the tumor gene based on the support vector machine[J];西安电子科技大学学报;2012-01
4 TANG Shi-xing~1,CHEN Jun~2,KE Feng-qin~3 (1.Personnel Division of Chengde Petroleum College,Chengde 067000,China) (2.Department of Medical Statistics,Third Military Medical University,Chongqing 400038,China) (3.Department of Automotive Engineering,Chengde Petroleum College,Chengde 067000,China);On the Fuzzy Clustering of the Cerebellar gene Based on FCM Algorithm[J];数学的实践与认识;2010-12
5 WANG Xin-jin1,ZHANG Hua2,CAO Xiang-hong1,CUI Guang-zhao1 1.School of Electrical and Information Engineering,Zhengzhou University of Light Industry,Zhengzhou 450002,China 2.School of Electrical Engineering,Henan University of Technology,Zhengzhou 450007,China;Wavelet packet decomposition-based on fuzzy clustering for gene expression data[J];计算机工程与应用;2009-19
6 WANG Wen-jun,ZHANG Jun-ying(School of Computer Science and Technology,Xidian Univ.,Xi'an 710071,China);New method for clustering gene expression data[J];西安电子科技大学学报;2009-03
7 ZHANG Hui1 FANG Zhao-qin2 GUAN Dong-yuan2 ZHAO Xiao-zhen3 KAN Wei-bing4 WU Zhong-hua2 GAO Bi-feng51.Research Center for Traditional Chinese Medicine Complexity System,Shanghai University of Traditional Chinese Medicine2.Basic Medical School,Shanghai University of Traditional Chinese Medicine3.Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine4.Putuo Hospital Affiliated to Shanghai University of Traditional Chinese Medicine5.Medical School of Klorada Universtity,Derfou,Clorid;Effects of Different TCM Therapeutic Methods on Expression of Related Cyclins and CDK4 in Rats of Liver Cancer[J];上海中医药大学学报;2009-03
8 ZHUO Shao-yuan, FANG Zhao-qin, GUAN Dong-yuan, et al. (Department of Laboratory Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China);Expression Characteristics of Cytochrome Superfamily Genes during Diethylnitrosamine-induced Hepatocarcinogenesis in Rats[J];中国肿瘤;2008-10
9 YANG De-Wu1, LI Xia1,2, XIAO Xue1, YANG Yue-Ying1, WANG Jing1 1. Department of Biological Engineering, Capital Medical University, Beijing 100069, China; 2. Department of Bioinformatics, Harbin Medical University, Harbin 150081, China;Association between ion channel subtype and its gene co-expression[J];遗传;2008-09
10 LIU Qi1,2,ZHANG Yin3,YU Rong-dong1,2,WANG Ming-yi4,YE Xiu-zi3(1.College of Life Sciences,Zhejiang University,Hangzhou 310058 China;2.Zhejiang-California International Nanosystems Institute,Zhejiang University, Hangzhou 310029,China;3.College of Computer Science and Technology,Zhejiang University,Hangzhou 310027,China;4.Cereal Research Centre,Winnipeg,MB Canada);Normalization methods for high-density oligonucleotide microarray data[J];浙江大学学报(工学版);2008-09
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