Bioinformatics in the post-genomics era: Towards Biology of the Systems

A grand challenge in genome science of the 21 century is to computationally predict systemic functional behaviors of the cell, organism, and the ecosystem from genomics and molecular information, especially for the purpose of medical, industrial, and other practical applications. This will require new bioinformatics, not simply for screening the large-scale data, but rather for reconstructing the system and computing its interactions with environment. While traditional genomics and other types of –omics approaches have contributed to our understanding of the genomics space of possible genes and proteins that make up the biological systems, new chemical genomics initiatives will give us glimpse of the chemical space of possible compounds and reactions and pathways that exist as an interface between the biological systems and the natural environment. The goal of this approach is to develop a ‘‘Life Simulator’’, which will be attained, step by step, hierarchically from subsystem simulators of subcellular mechanisms, whole cell simulators, cell development simulators, organ simulators, physiological simulators, pathological simulators to body simulators. An ultimate goal of bioinformatics in next decade is a complete computer representation of the cell, the organism, and the biosphere, which will enable computational prediction of higher-level complexity, such as molecular interaction networks involving various cellular processes and Phenotypes (morphological, physiological, and behavioral aspects) of entire organisms. To increase our understanding of cellular processes from genome information, pathway database, for example KEGG and EGENES have been created in the past decade. Whereas most databases concentrate on molecular properties (for example, sequences, 3D structures, motifs and gene expressions), these databases tackle complex cellular properties, such as metabolism, signal transduction and cell cycle, by storing the corresponding networks of interacting molecules in computerized forms, often as graphical pathway diagrams. In this review we will introduce KEGG and EGENES as an example for knowledge based system for efficient analysis of genes and ESTs, linking genomic information with higher order functional information in a single ناريا يملاسا يروهجم يژولونكتويب يلم شياهم ينمجنپ 5 3 هام رذآ 1386 نارس سلاجا نلاس ، The 5 National Biotechnology Congress of Iran 24-26 Nov, 2007, Summit Meeting Conference Hall, TehranIran 2 database. The higher order functional information in these databases are stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, genetic information processing, environmental information processing, and cellular process.