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ning145301金虫 (正式写手)
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求助，帮忙查一篇SCI文章的检索证明，非常感谢！已有2人参与
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文章题目：A network-based approach to identify disease-associated gene modules through integrating DNA methylation and gene expression 期刊： Biochemical and Biophysical Research Communications 卷期号及页码：2015，465(3): 437-442 非常感谢！ |
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lilyjr
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ning145301: 金币+5, ★★★★★最佳答案 2015-11-14 20:38:54
感谢参与，应助指数 +1
ning145301: 金币+5, ★★★★★最佳答案 2015-11-14 20:38:54
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A network-based approach to identify disease-associated gene modules through integrating DNA methylation and gene expression 作者:Zhang, YY (Zhang, Yuanyuan)[ 1 ] ; Zhang, JY (Zhang, Junying)[ 1 ] ; Liu, ZW (Liu, Zhaowen)[ 1 ] ; Liu, YJ (Liu, Yajun)[ 1 ] ; Tuo, SH (Tuo, Shouheng)[ 1 ] BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 卷: 465 期: 3 页: 437-442 DOI: 10.1016/j.bbrc.2015.08.033 出版年: SEP 25 2015 查看期刊信息 摘要 Formation and progression of complex diseases are generally the joint effect of genetic and epigenetic disorders, thus an integrative analysis of epigenetic and genetic data is essential for understanding mechanism of the diseases. In this study, we integrate Illuminate 450k DNA methylation and gene expression data to calculate the weights of gene network using Principal Component Analysis (PCA) and Canonical Correlation Analysis (CCA). The approach considers all methylation values of CpG sites in a gene, rather than averaging them which was used in other studies ignoring the variability of the methylation sites. Through comparing topological features of control network with those of case network, including global and local features, candidate disease-associated genes and gene modules are identified. We apply the approach to real data, breast invasive carcinoma (BRCA). It successfully identifies susceptibility breast cancer-related genes, such as TP53, BRCA1, EP300, CDK2, MCM7 and so forth, within which most are previously known to breast cancer. Also, GO and pathway enrichment analysis indicate that these genes enrich in cell apoptosis and regulation of cell death which are cancer-related biological processes. Importantly, through analyzing the functions and comparing expression and methylation values of these genes between cases and controls, we find some genes, such as VASN, SNRPD3, and gene modules, targeted by POLR2C, CHMP1B and TAF9, which might be novel breast cancer-related biomarkers. (C) 2015 Elsevier Inc. All rights reserved. 关键词 作者关键词  NA methylation; Gene expression; Gene network; Integrative analysis; Canonical correlation analysisKeyWords Plus:BREAST-CANCER; PROMOTER METHYLATION; CELL; GENOME; IDENTIFICATION; VALIDATION; MICROARRAY 作者信息 通讯作者地址: Zhang, JY (通讯作者) [显示增强组织信息的名称] Xidian Univ, Sch Comp Sci & Technol, Xian 710071, Peoples R China. 地址: [显示增强组织信息的名称] [ 1 ] Xidian Univ, Sch Comp Sci & Technol, Xian 710071, Peoples R China 电子邮件地址:jyzhang@mail.xidian.edu.cn 基金资助致谢 基金资助机构 授权号 Natural Science Foundation of China 61070137 61201312 61170183 Research Fund for the Doctoral Program of Higher Education of China 20130203110017 Fundamental Research Funds for the Central Universities of China BDY171416 JB140306 查看基金资助信息 出版商 ACADEMIC PRESS INC ELSEVIER SCIENCE, 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA 类别 / 分类 研究方向:Biochemistry & Molecular Biology; Biophysics Web of Science 类别:Biochemistry & Molecular Biology; Biophysics 文献信息 文献类型:Article 语种:English 入藏号: WOS:000361418300020 PubMed ID: 26282201 ISSN: 0006-291X eISSN: 1090-2104 期刊信息 Impact Factor (影响因子): Journal Citation Reports® 其他信息 IDS 号: CR5XS Web of Science 核心合集中的 "引用的参考文献": 31 Web of Science 核心合集中的 "被引频次": 0 |
2楼2015-11-14 10:28:12
nidewuliang
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ning145301: 金币+5, ★★★★★最佳答案 2015-11-14 20:39:09
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ning145301: 金币+5, ★★★★★最佳答案 2015-11-14 20:39:09
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A network-based approach to identify disease-associated gene modules through integrating DNA methylation and gene expression 作者:Zhang, YY (Zhang, Yuanyuan)[ 1 ] ; Zhang, JY (Zhang, Junying)[ 1 ] ; Liu, ZW (Liu, Zhaowen)[ 1 ] ; Liu, YJ (Liu, Yajun)[ 1 ] ; Tuo, SH (Tuo, Shouheng)[ 1 ] BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 卷: 465 期: 3 页: 437-442 DOI: 10.1016/j.bbrc.2015.08.033 出版年: SEP 25 2015 查看期刊信息 BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 影响因子 2.297 2.382 2014 5 年 JCR® 类别 类别中的排序 JCR 分区 BIOCHEMISTRY & MOLECULAR BIOLOGY 180/290 Q3 BIOPHYSICS 41/73 Q3 数据来自第 2014 版 Journal Citation Reports® 出版商 ACADEMIC PRESS INC ELSEVIER SCIENCE, 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA ISSN: 0006-291X eISSN: 1090-2104 研究领域 Biochemistry & Molecular Biology Biophysics 摘要 Formation and progression of complex diseases are generally the joint effect of genetic and epigenetic disorders, thus an integrative analysis of epigenetic and genetic data is essential for understanding mechanism of the diseases. In this study, we integrate Illuminate 450k DNA methylation and gene expression data to calculate the weights of gene network using Principal Component Analysis (PCA) and Canonical Correlation Analysis (CCA). The approach considers all methylation values of CpG sites in a gene, rather than averaging them which was used in other studies ignoring the variability of the methylation sites. Through comparing topological features of control network with those of case network, including global and local features, candidate disease-associated genes and gene modules are identified. We apply the approach to real data, breast invasive carcinoma (BRCA). It successfully identifies susceptibility breast cancer-related genes, such as TP53, BRCA1, EP300, CDK2, MCM7 and so forth, within which most are previously known to breast cancer. Also, GO and pathway enrichment analysis indicate that these genes enrich in cell apoptosis and regulation of cell death which are cancer-related biological processes. Importantly, through analyzing the functions and comparing expression and methylation values of these genes between cases and controls, we find some genes, such as VASN, SNRPD3, and gene modules, targeted by POLR2C, CHMP1B and TAF9, which might be novel breast cancer-related biomarkers. (C) 2015 Elsevier Inc. All rights reserved. 关键词 作者关键词 NA methylation; Gene expression; Gene network; Integrative analysis; Canonical correlation analysis KeyWords Plus:BREAST-CANCER; PROMOTER METHYLATION; CELL; GENOME; IDENTIFICATION; VALIDATION; MICROARRAY 作者信息 通讯作者地址: Zhang, JY (通讯作者) Xidian Univ, Sch Comp Sci & Technol, Xian 710071, Peoples R China. 增强组织信息的名称 Xidian University 地址: [ 1 ] Xidian Univ, Sch Comp Sci & Technol, Xian 710071, Peoples R China 增强组织信息的名称 Xidian University 电子邮件地址:jyzhang@mail.xidian.edu.cn 基金资助致谢 基金资助机构 授权号 Natural Science Foundation of China 61070137 61201312 61170183 Research Fund for the Doctoral Program of Higher Education of China 20130203110017 Fundamental Research Funds for the Central Universities of China BDY171416 JB140306 查看基金资助信息关闭基金资助信息 This work was supported by the Natural Science Foundation of China under Grants 61070137, 61201312, 61170183, Research Fund for the Doctoral Program of Higher Education of China (No. 20130203110017), and the Fundamental Research Funds for the Central Universities of China (No. BDY171416, JB140306). 出版商 ACADEMIC PRESS INC ELSEVIER SCIENCE, 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA 类别 / 分类 研究方向:Biochemistry & Molecular Biology; Biophysics Web of Science 类别:Biochemistry & Molecular Biology; Biophysics 文献信息 文献类型:Article 语种:English 入藏号: WOS:000361418300020 PubMed ID: 26282201 ISSN: 0006-291X eISSN: 1090-2104 期刊信息 Impact Factor (影响因子): Journal Citation Reports® 数据来自第 2014 版 Journal Citation Reports® 其他信息 IDS 号: CR5XS Web of Science 核心合集中的 "引用的参考文献": 31 Web of Science 核心合集中的 "被引频次": 0 |
3楼2015-11-14 10:42:39
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