Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle

Background: A transcriptional regulatory module (TRM) is a set of genes that is regulated by a common set of transcription factors (TFs). By organizing the genome into TRMs, a living cell can coordinate the activities of many genes and carry out complex functions. Therefore, identifying TRMs is helpful for understanding gene regulation. Results: Integrating gene expression and ChIP-chip data, we develop a method, called MOdule Finding Algorithm (MOFA), for reconstructing TRMs of the yeast cell cycle. MOFA identified 87 TRMs, which together contain 336 distinct genes regulated by 40 TFs. Using various kinds of data, we validated the biological relevance of the identified TRMs. Our analysis shows that different combinations of a fairly small number of TFs are responsible for regulating a large number of genes involved in different cell cycle phases and that there may exist crosstalk between the cell cycle and other cellular processes. MOFA is capable of finding many novel TF-target gene...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Wei-Sheng Wu, Wen-Hsiung Li, Bor-Sen Chen
• Keywords: BMCBI 2006, Cell Cycle, Transcriptional Regulatory Module, Yeast Cell Cycle