title: Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria.
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 ( A: cross- BA: cteria SY: stems) 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.
authors.affiliation: Group of Regulatory Systems Biology, Evolutionary Genomics Program, Universidad Nacional Autónoma De México, Av. Universidad S/N, Col. Chamilpa, Cuernavaca, Morelos 62210, México Undergraduate Program in Genomic Sciences, Center for Genomics Sciences, Universidad Nacional Autónoma De México, Av. Universidad S/N, Col. Chamilpa, Cuernavaca, Morelos 62210, México.
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Ibarra-Arellano
authors.affiliation: Group of Regulatory Systems Biology, Evolutionary Genomics Program, Universidad Nacional Autónoma De México, Av. Universidad S/N, Col. Chamilpa, Cuernavaca, Morelos 62210, México Undergraduate Program in Genomic Sciences, Center for Genomics Sciences, Universidad Nacional Autónoma De México, Av. Universidad S/N, Col. Chamilpa, Cuernavaca, Morelos 62210, México.
authors.forename: Adrián I
authors.initials: AI
authors.lastname: Campos-González
authors.affiliation: Departamento De Tecnología Ambiental, Universidad Politécnica Del Estado De Morelos, Blvd. Cuauhnáhuac 566, Col. Lomas Del Texcal, Jiutepec, Morelos 62550, México.
authors.forename: Luis G
authors.initials: LG
authors.lastname: Treviño-Quintanilla
authors.affiliation: Centrum Für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, Bielefeld, 33615, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Tauch
authors.affiliation: Group of Regulatory Systems Biology, Evolutionary Genomics Program, Universidad Nacional Autónoma De México, Av. Universidad S/N, Col. Chamilpa, Cuernavaca, Morelos 62210, México jfreyre@ccg.unam.mx.
authors.forename: Julio A
authors.initials: JA
authors.lastname: Freyre-González
mesh_terms: D001419:Bacteria / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D030541:Databases, Genetic; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics*; D053263:Gene Regulatory Networks; D016680:Genome, Bacterial / Q000235:genetics*; D020407:Internet