collective dynamics of specific gene ensembles crucial for neutrophil differentiation the existence of genome vehicles revealed特定基因的集体动力学乐团中性粒细胞分化的关键基因组显示车辆的存在.pdf

Collective Dynamics of Specific Gene Ensembles Crucial for Neutrophil Differentiation: The Existence of Genome Vehicles Revealed 1,2 . 1,2. 3 1,2 1,2 . Masa Tsuchiya * , Vincent Piras , Alessandro Giuliani , Masaru Tomita , Kumar Selvarajoo * 1 Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan, 2 School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan, ´ 3 Environment and Health Department, Istituto Superiore di Sanita, Rome, Italy Abstract Cell fate decision remarkably generates specific cell differentiation path among the multiple possibilities that can arise through the complex interplay of high-dimensional genome activities. The coordinated action of thousands of genes to switch cell fate decision has indicated the existence of stable attractors guiding the process. However, origins of the intracellular mechanisms that create ‘‘cellular attractor’’ still remain unknown. Here, we examined the collective behavior of genome-wide expressions for neutrophil differentiation through two different stimuli, dimethyl sulfoxide (DMSO) and all- trans-retinoic acid (atRA). To overcome the difficulties of dealing with single gene expression noises, we grouped genes into ensembles and analyzed their expression dynamics in correlation space defined by Pearson correlation and mutual information. The standard deviation of correlation distributions of gene ensembles reduces when the ensemble size is increased following the inverse square root law, for both ensembles chosen ran