Abstract
The availability of databases electronically encoding curated regulatory networks and of high-throughput technologies and methods to discover regulatory interactions provides an invaluable source of data to understand the principles underpinning the organization and evolution of these networks responsible for cellular regulation. Nevertheless, data on these sources never goes beyond the regulon level despite the fact that regulatory networks are complex hierarchical-modular structures still challenging our understanding. This brings the necessity for an inventory of systems across a large range of organisms, a key step to rendering feasible comparative systems biology approaches. In this work, we take the first step towards a global understanding of the regulatory networks organization by making a cartography of the functional architectures of diverse bacteria. Abasy (Across-bacteria systems) Atlas provides a comprehensive inventory of annotated functional systems, global network properties and systems-level elements (global regulators, modular genes shaping functional systems, basal machinery genes and intermodular genes) predicted by the natural decomposition approach for reconstructed and meta-curated regulatory networks across a large range of bacteria, including pathogenically and biotechnologically relevant organisms. The meta-curation of regulatory datasets provides the most complete and reliable set of regulatory interactions currently available, which can even be projected into subsets by considering the force or weight of evidence supporting them or the systems that they belong to. Besides, Abasy Atlas provides data enabling large-scale comparative systems biology studies aimed at understanding the common principles and particular lifestyle adaptions of systems across bacteria. Abasy Atlas contains systems and system-level elements for 50 regulatory networks comprising 78 649 regulatory interactions covering 42 bacteria in nine taxa, containing 3708 regulons and 1776 systems. All this brings together a large corpus of data that will surely inspire studies to generate hypothesis regarding the principles governing the evolution and organization of systems and the functional architectures controlling them.Database URL: http://abasy.ccg.unam.mx
Highlights
Bacterial regulatory networks (RNs) are responsible for sense stimuli and environmental cues and respond
The decomposition of diverse RNs into their systems and systems-level elements beyond the regulon allows unraveling the complexity of these networks and provides new insights into the organizational principles governing them
The two most-complete RN models in Abasy Atlas are our metacurations for M. tuberculosis H37Rv (77%) and B. subtilis 168 (75%)
Summary
Bacterial regulatory networks (RNs) are responsible for sense stimuli and environmental cues and respond . The development of high-throughput interaction discovery methodologies (e.g. ChIP-seq) and gene-expression-based methods for inference of RNs has produced novel regulatory datasets with high genomic coverage Examples of this are the datasets for B. subtilis 168, M. tuberculosis H37Rv and P. aeruginosa PAO1 found in our literature review described above (Table 1). These novel meta-curated datasets represent the most complete RNs currently reported for B. subtilis 168, M. tuberculosis H37Rv and P. aeruginosa PAO1, as determined by their genomic coverage: 75, 77 and 16%, respectively These meta-curated regulatory networks, regardless of their coverage, exhibit properties that characterize hierarchical-modular RNs (see their global network properties in Abasy Atlas) [10, 11]. Six tables store functional data extracted from external sources (gos, goa, cogs, cog_families, cog_classes and cog)
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