(Hypotheses and Open Problems revealed by Subsystems)
Sequencing and analysis of hundreds, soon to be thousands, of genomes reveals multiple gaps in our knowledge of basic biochemical and cellular processes. Accurate mapping of the revealed open problems within a framework of specific subsystems and groups of organisms sets the stage for generating hypotheses amenable to experimental validation. In a growing number of cases, predictions of novel genes and pathways delivered by comparative genomics techniques (eg analysis of gene clustering on prokaryotic chromosomes) get successfully verified.
EGGS database: Essential Genes on Genome Scale
SEED maintains an up-to-date database of all microbial gene essentiality data experimentally obtained in the currently published genome-scale gene essentiality screens (listed in Table 1). Comparative analysis of these data across multiple organisms in a rich genomic, biochemical, and phylogenetic contexts provided by the collection of annotated Subsystems greatly facilitates their interpretation and practical applications, such as, understanding of cellular networks, gene and pathway discovery, identification of novel drug targets, and strain engineering.