Abasy Atlas provides a comprehensive atlas of annotated functional systems (hereinafter also referred as modules), global network properties, and system-level elements predicted by the natural decomposition approach[1,2,3] (NDA) for reconstructed and meta-curated regulatory networks across a large range of bacteria, including pathogenic and biotechnologically relevant organisms. Regulatory networks could be thought of as a “take decisions” organ in bacteria. They not only sense stimulus and respond accordingly but, for example, in a complex environment, they “take composite decisions” to prioritize the assimilation and catabolism of carbon sources according to the metabolic preferences of each organism. To accomplish this, RNs composed by thousands of regulatory interactions, must follow well-defined organization principles governing their dynamics.
In the last decades of the 20th century, the first levels of gene organization were unveiled as the operon and the regulon. Currently, a few databases (RegulonDB, SubtiWiki, DBTBS, CoryneRegNet, and RegTransBase) extract, by manual curation of literature, the molecular knowledge about gene regulation in different organisms providing an invaluable source of information. Nevertheless, information on these databases never goes beyond the regulon level, whereas cumulative evidence has showed that regulatory networks are complex hierarchical-modular networks whose organizational and evolutionary principles are pivotal for determining the dynamics of the cell and still challenging our understanding. In this atlas, we take the first step towards a global understanding of the regulatory networks organization by building a cartography of the functional architecture for each of the best-studied organisms.
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The NDA defines criteria to identify systems and system-level elements in a regulatory network, and rules to reveal its functional architecture by controlled decomposition (Figure 1). This biologically motivated approach mathematically derives the architecture and system-level elements from the global structural properties of a given regulatory network. It is based on two biological premises:
A module is a set of genes cooperating to carry out a particular physiological function, thus conferring different phenotypic traits to the cell.
Given the pleiotropic effect of global regulators, they must not belong to modules but rather coordinate them in response to general-interest environmental cues.
According to this approach, every gene in a regulatory network is predicted to belong to one out of four possible classes of system-level elements, which interrelate in a non-pyramidal, three-tier, hierarchy shaping the functional architecture as follows[1,2,3]: (1) Global regulators are responsible for coordinating both the (2) basal cell machinery, composed of exclusively globally regulated genes (EGRGs), and (3) locally autonomous modules (shaped by modular genes), whereas (4) intermodular genes integrate, at promoter level, physiologically disparate module responses eliciting a combinatorial processing of environmental cues (Figure 2).
Abasy Atlas is actively developed by the Regulatory Systems Biology Research Group at the Program of Evolutionary Genomics, Center for Genomic Sciences (CCG), UNAM:
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