Global analysis of the regulatory network structure of
gene expression in Saccharomyces cerevisiae

Wataru Gunji , Takahito Kai , Yoriko Takahashi , Yukihiro Maki , Wataru Kurihara ,
Takahiko Utsugi
, Fumihiro Fujimori , Yasufumi Murakami

DNA Research

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 transcriptional 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 four hundred transcriptional factors into three groups based on their expression profiles. We then analyzed the effect of the loss of function of various induced transcriptional factors on the global expression profile, under 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 transcriptional 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 timely and conditional manner.

Microarray Supplement data

Supplemental data 1

Expression profiles data of disrupted transcription factors.

Supplemental data 2

Expression profiles data of all genes under 16 culture conditions.

Supplemental data 3

Expression profiles data of transcription factors under 16 culture conditions.

Laboratory of Genome Biology
Department of Biological Science & Technology
Faculty of Industrial Science & Technology

Tokyo University of Science