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Nucleic Acids Research 2005 33(Web Server Issue):W659-W664; doi:10.1093/nar/gki446
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© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

ASIAN: a web server for inferring a regulatory network framework from gene expression profiles

Sachiyo Aburatani, Kousuke Goto1, Shigeru Saito1, Hiroyuki Toh2 and Katsuhisa Horimoto*

Laboratory of Biostatistics, Institute of Medical Science, University of Tokyo 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan 1Bioscience Department, INFOCOM CORPORATION Mitsui Sumitomo Insurance Surugadai Annex Building, 3-11, Kanda-surugadai, Chiyoda-ku, Tokyo 101-0062, Japan 2Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan

*To whom correspondence should be addressed. Tel: +81 3 5449 5466; Fax: +81 3 3442 3654; Email: khorimot{at}ims.u-tokyo.ac.jp

Received February 14, 2005. Revised March 30, 2005. Accepted March 30, 2005.

The standard workflow in gene expression profile analysis to identify gene function is the clustering by various metrics and techniques, and the following analyses, such as sequence analyses of upstream regions. A further challenging analysis is the inference of a gene regulatory network, and some computational methods have been intensively developed to deduce the gene regulatory network. Here, we describe our web server for inferring a framework of regulatory networks from a large number of gene expression profiles, based on graphical Gaussian modeling (GGM) in combination with hierarchical clustering (http://eureka.ims.u-tokyo.ac.jp/asian). GGM is based on a simple mathematical structure, which is the calculation of the inverse of the correlation coefficient matrix between variables, and therefore, our server can analyze a wide variety of data within a reasonable computational time. The server allows users to input the expression profiles, and it outputs the dendrogram of genes by several hierarchical clustering techniques, the cluster number estimated by a stopping rule for hierarchical clustering and the network between the clusters by GGM, with the respective graphical presentations. Thus, the ASIAN (Automatic System for Inferring A Network) web server provides an initial basis for inferring regulatory relationships, in that the clustering serves as the first step toward identifying the gene function.


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