Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization.

Escorcia-Rodriguez JM, Tauch A, Freyre-Gonzalez JA (2020)
Computational and structural biotechnology journal 18: 1228-1237.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Autor*in
Escorcia-Rodriguez, Juan M; Tauch, AndreasUniBi; Freyre-Gonzalez, Julio A
Abstract / Bemerkung
Some organism-specific databases about regulation in bacteria have become larger, accelerated by high-throughput methodologies, while others are no longer updated or accessible. Each database homogenize its datasets, giving rise to heterogeneity across databases. Such heterogeneity mainly encompasses different names for a gene and different network representations, generating duplicated interactions that could bias network analyses. Abasy (Across-bacteria systems) Atlas consolidates information from different sources into meta-curated regulatory networks in bacteria. The high-quality networks in Abasy Atlas enable cross-organisms analyses, such as benchmarking studies where gold standards are required. Nevertheless, network incompleteness still casts doubts on the conclusions of network analyses, and available sampling methods cannot reflect the curation process. To tackle this problem, the updated version of Abasy Atlas presented in this work provides historical snapshots of regulatory networks. Thus, network analyses can be performed at different completeness levels, making possible to identify potential bias and to predict future results. We leverage the recently found constraint in the complexity of regulatory networks to develop a novel model to quantify the total number of regulatory interactions as a function of the genome size. This completeness estimation is a valuable insight that may aid in the daunting task of network curation, prediction, and validation. The new version of Abasy Atlas provides 76 networks (204,282 regulatory interactions) covering 42 bacteria (64% Gram-positive and 36% Gram-negative) distributed in 9 species (Mycobacterium tuberculosis, Bacillus subtilis, Escherichia coli, Corynebacterium glutamicum, Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pyogenes, Streptococcus pneumoniae, and Streptomyces coelicolor), containing 8459 regulons and 4335 modules. Database URL: https://abasy.ccg.unam.mx/. © 2020 The Author(s).
Erscheinungsjahr
2020
Zeitschriftentitel
Computational and structural biotechnology journal
Band
18
Seite(n)
1228-1237
eISSN
2001-0370
Page URI
https://pub.uni-bielefeld.de/record/2944331

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Escorcia-Rodriguez JM, Tauch A, Freyre-Gonzalez JA. Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization. Computational and structural biotechnology journal. 2020;18:1228-1237.
Escorcia-Rodriguez, J. M., Tauch, A., & Freyre-Gonzalez, J. A. (2020). Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization. Computational and structural biotechnology journal, 18, 1228-1237. doi:10.1016/j.csbj.2020.05.015
Escorcia-Rodriguez, J. M., Tauch, A., and Freyre-Gonzalez, J. A. (2020). Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization. Computational and structural biotechnology journal 18, 1228-1237.
Escorcia-Rodriguez, J.M., Tauch, A., & Freyre-Gonzalez, J.A., 2020. Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization. Computational and structural biotechnology journal, 18, p 1228-1237.
J.M. Escorcia-Rodriguez, A. Tauch, and J.A. Freyre-Gonzalez, “Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization.”, Computational and structural biotechnology journal, vol. 18, 2020, pp. 1228-1237.
Escorcia-Rodriguez, J.M., Tauch, A., Freyre-Gonzalez, J.A.: Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization. Computational and structural biotechnology journal. 18, 1228-1237 (2020).
Escorcia-Rodriguez, Juan M, Tauch, Andreas, and Freyre-Gonzalez, Julio A. “Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization.”. Computational and structural biotechnology journal 18 (2020): 1228-1237.

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