Augusta: From RNA-Seq to Gene Regulatory Networks and Boolean Models
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26220%2F24%3APU150245" target="_blank" >RIV/00216305:26220/24:PU150245 - isvavai.cz</a>
Result on the web
<a href="https://www.sciencedirect.com/science/article/pii/S2001037024000138?via%3Dihub" target="_blank" >https://www.sciencedirect.com/science/article/pii/S2001037024000138?via%3Dihub</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1016/j.csbj.2024.01.013" target="_blank" >10.1016/j.csbj.2024.01.013</a>
Alternative languages
Result language
angličtina
Original language name
Augusta: From RNA-Seq to Gene Regulatory Networks and Boolean Models
Original language description
Computational models of gene regulations help to understand regulatory mechanisms and are extensively used in a wide range of areas, e.g., biotechnology or medicine, with significant benefits. Unfortunately, there are only a few computational gene regulatory models of whole genomes allowing static and dynamic analysis due to the lack of sophisticated tools for their reconstruction. Here, we describe Augusta, an open-source Python package for Gene Regulatory Network (GRN) and Boolean Network (BN) inference from the high-throughput gene expression data. Augusta can reconstruct genome-wide models suitable for static and dynamic analyses. Augusta uses a unique approach where the first estimation of a GRN inferred from expression data is further refined by predicting transcription factor binding motifs in promoters of regulated genes and by incorporating verified interactions obtained from databases. Moreover, a refined GRN is transformed into a draft BN by searching in the curated model database and setting logical rules to incoming edges of target genes, which can be further manually edited as the model is provided in the SBML file format. The approach is applicable even if information about the organism under study is not available in the databases, which is typically the case for non-model organisms including most microbes. Augusta can be operated from the command line and, thus, is easy to use for automated prediction of models for various genomes. The Augusta package is freely available at github.com/JanaMus/Augusta. Documentation and tutorials are available at augusta.readthedocs.io.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Result continuities
Project
<a href="/en/project/GA22-10845S" target="_blank" >GA22-10845S: Unraveling the role of polyhydroxyalkanoates in Schlegelella thermodepolymerans – promising environmental bacterium for next generation biotechnology</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2024
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Computational and Structural Biotechnology Journal
ISSN
2001-0370
e-ISSN
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Volume of the periodical
23
Issue of the periodical within the volume
December 2024
Country of publishing house
SE - SWEDEN
Number of pages
8
Pages from-to
783-790
UT code for WoS article
001174569000001
EID of the result in the Scopus database
2-s2.0-85185178942