A Study of Genomic Modules and Intermodular Networks for Understanding the Operating System of Life

Higher eukaryotes’ phenotypes–the unique properties of a system composed of several genes and their relations–are entirely different from a set of properties of individual genes. During evolution, higher organisms’ genes become multipurpose and their phenotypic implication become abstract. We hypothesize that an operating system of life (OSL) exists in “genome space,” encoding a variety of phenotypes and realizing them through chemical circuits in “material space.” Genes’ generalization and abstraction explain the necessity of “genomic modules,” each of which encodes a unitary phenotype as a subroutine in the OSL. A genetic network is a projection map of the OSL’s active modules on the interface between the two spaces. We searched for genomic modules and intermodular networks developed in differentiating cells with the density matrix that mathematically defines a state of the system composed of genes and their relations, and demonstrated the modules’ relevance to the phenotypes of differentiating cells.