Learning module networks from genome-wide location and expression data
文献类型：期刊论文
| 作者 | Xu, XJ; Wang, LS; Ding, DF |
| 刊名 | FEBS LETTERS
 |
| 出版日期 | 2004 |
| 卷号 | 578期号:3页码:297-304 |
| 关键词 | module network regulatory program location probability |
| 通讯作者 | Ding, DF (reprint author), Chinese Acad Sci, Grad Sch, Shanghai Inst Biol Sci, Inst Biochem & Cell Biol,Key Lab Proteom, Shanghai 200031, Peoples R China.,xjxu@sibs.ac.cn ; dingdafu@server.shcnc.ac.cn |
| 英文摘要 | We develop a systematic algorithm for discovering network of regulatory modules, which identifies regulatory modules and their regulation program by integrating genome-wide location and expression data. Unlike previous approaches [Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) Proc. Natl. Acad. Sci. USA 95, 14863-14868; Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J. and Church, G.M. (1999) Nat. Genet. 22, 281-285; Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y. and Barkai, N. (2002) Nat. Genet. 31, 370-377; Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D. and Friedman, N. (2003) Nat. Genet. 34, 166-176] that relied primarily on gene expression data, our algorithm regards the regulator binding data as prior knowledge that provide direct evidence of physical regulatory interactions. We applied the method to a Saccharomyces cerevisiae genome-wide location data [Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, L, Zeitlinger, J., Jennings, E.G., Murray, H.L. Gordon, D.B., Ren, B., Wyrick, J.J., Tagne, J.B., Volkert, T.L., Fraenkel, E., Gifford, D.K. and Young, R.A. (2002) Science 298, 799-804] for 106 DNA-binding transcription factors and 250 gene expression experiments under the conditions from the cell cycle to responses to various stress conditions. The results show that our method is able to identify functionally coherent modules and their proper regulators. Supplementary materials are available at http://compbio.sibsnet.org/ projects/module-network/. (C) 2004 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. |
| 学科主题 | Biochemistry & Molecular Biology; Biophysics; Cell Biology |
| 类目[WOS] | Biochemistry & Molecular Biology ; Biophysics ; Cell Biology |
| 关键词[WOS] | YEAST SACCHAROMYCES-CEREVISIAE ; CATABOLITE REPRESSION ; REGULATORY NETWORKS ; BAYESIAN NETWORKS ; CLUSTER-ANALYSIS ; PROTEIN ; GENES ; IDENTIFICATION ; REPLICATION ; SUBUNIT |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000225939900018 |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.143/handle/331003/2049]  |
| 专题 | 上海生化细胞研究所_上海生科院生化细胞研究所 |
| 推荐引用方式 GB/T 7714 | Xu, XJ,Wang, LS,Ding, DF. Learning module networks from genome-wide location and expression data[J]. FEBS LETTERS,2004,578(3):297-304. |
| APA | Xu, XJ,Wang, LS,&Ding, DF.(2004).Learning module networks from genome-wide location and expression data.FEBS LETTERS,578(3),297-304. |
| MLA | Xu, XJ,et al."Learning module networks from genome-wide location and expression data".FEBS LETTERS 578.3(2004):297-304. |
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