Revealing the gene regulatory systems among DNA and proteins in living cells is one of the central aims of systems biology. In this study, I used Structural Equation Modeling (SEM) in combination with stepwise factor analysis to infer the protein-DNA interactions for gene expression control from only gene expression profiles, in the absence of protein information. I applied my approach to infer the causalities within the well-studied serial transcriptional regulation composed of GAL-related genes in yeast. This allowed me to reveal the hierarchy of serial transcriptional regulation, including previously unclear protein-DNA interactions. The validity of the constructed model was demonstrated by comparing the results with previous reports describing the regulation of the transcription factors. Furthermore, the model revealed combinatory regulation by Gal4p and Gal80p. In this study, the target genes were divided into three types: those regulated by one factor and those controlled by a combination of two factors.
PDF (671.33 KB PDF FORMAT)
RIS citation (ENDNOTE, REFERENCE MANAGER, PROCITE, REFWORKS)
BibTex citation (BIBDESK, LATEX)
Publishing in Gene Regulation and Systems Biology was a very positive experience. I was impressed by the fast and uncomplicated submission process as well as the clear and professional peer review process which helped to improve the manuscript. The Libertas Academica team was very patient and helpful. I would definitely recommend the journal to other colleagues in the field!