a novel method to identify cooperative functional modules study of module coordination in the saccharomyces cerevisiae cell cycle一个新颖的方法来识别模块协调的合作功能模块研究酿酒酵母细胞周期.pdfVIP

Hsu et al. BMC Bioinformatics 2011, 12:281 /1471-2105/12/281 METHODOLOGY ARTICLE Open Access A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle 1 2 3 4,5* 1,6* Jeh-Ting Hsu , Chien-Hua Peng , Wen-Ping Hsieh , Chung-Yu Lan and Chuan Yi Tang Abstract Background: Identifying key components in biological processes and their associations is critical for deciphering cellular functions. Recently, numerous gene expression and molecular interaction experiments have been reported in Saccharomyces cerevisiae, and these have enabled systematic studies. Although a number of approaches have been used to predict gene functions and interactions, tools that analyze the essential coordination of functional components in cellular processes still need to be developed. Results: In this work, we present a new approach to study the cooperation of functional modules (sets of functionally related genes) in a specific cellular process. A cooperative module pair is defined as two modules that significantly cooperate with certain functional genes in a cellular process. This method identifies cooperative module pairs that significantly influence a cellular process and the correlated genes and interactions that are essential to that process. Using the yeast cell cycle as an example, we identified 101 cooperative module associations among 82 modules, and importantly, we established a cell cycle-specific cooperative module network. Most of the identified module pairs cover cooperative pathways and components essential to the cell cycle. We found that 14, 36, 18, 15, and 20 cooperative module pairs significantly cooperate with genes regulated in early