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DNA Research 2004 11(3):163-177; doi:10.1093/dnares/11.3.163
© 2004 by Kazusa DNA Research Institute
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Global Analysis of the Regulatory Network Structure of Gene Expression in Saccharomyces cerevisiae

Wataru Gunji1,2, Takahito Kai1,2, Yoriko Takahashi3, Yukihiro Maki3, Wataru Kurihara1,2, Takahiko Utsugi1,2, Fumihiro Fujimori1 and Yasufumi Murakami1,2,*

1Department of Biological Science & Technology, Faculty of Industrial Science & Technology, Tokyo University of Science 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
2Genome and Drug Discovery Research Center, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-0022, Japan
3R&D Dept., Bioscience Division, Mitsui Knowledge Industry Co., Ltd. 1-32-2 Honcho, Nakano-ku, Tokyo, 164-8721, Japan

* To whom correspondence should be addressed. Tel. +81-4-7124-1501 (Ext. 4408), Fax. +81-4-7122-1360, E-mail: yasufumi{at}rs.noda.tus.ac.jp

Gene expression in eukaryotic cells is controlled by the concerted action of various transcription factors. To help clarify these complex mechanisms, we attempted to develop a method for extracting maximal information regarding the transcriptional control pathways. To this end, we first analyzed the expression profiles of numerous transcription factors in yeast cells, under the assumption that the expression levels of these factors would be elevated under conditions in which the factors were active in the cells. Based on the results, we successfully categorized about 400 transcription factors into three groups based on their expression profiles. We then analyzed the effect of the loss of function of various induced transcription factors on the global expression profile to investigate the above-mentioned assumption of a correlation between transcription elevation and functional activity. By comparing the expression profiles of wild-type with those of disruption mutants using microarrays, we were able to detect a substantial number of relations between transcription factors and the genes they regulate. The results of these experiments suggested that our approach is useful for understanding the global transcriptional networks of eukaryotic cells, in which most genes are regulated in a temporal and conditional manner.

Key words: microarray; transcription factor; gene expression network; expression profiles


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