Detail publikace

Augusta: From RNA-Seq to Gene Regulatory Networks and Boolean Models

MUSILOVÁ, J. VAFEK, Z. PUNYIA, B. ZIMMER, R. HELIKAR, T. SEDLÁŘ, K.

Originální název

Augusta: From RNA-Seq to Gene Regulatory Networks and Boolean Models

Typ

článek v časopise ve Web of Science, Jimp

Jazyk

angličtina

Originální abstrakt

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.

Klíčová slova

Python package; gene interactions; mutual information; transcription factor; binding motifs; databases

Autoři

MUSILOVÁ, J.; VAFEK, Z.; PUNYIA, B.; ZIMMER, R.; HELIKAR, T.; SEDLÁŘ, K.

Vydáno

20. 1. 2024

Nakladatel

Elsevier

ISSN

2001-0370

Periodikum

Computational and Structural Biotechnology Journal

Ročník

23

Číslo

December 2024

Stát

Švédské království

Strany od

783

Strany do

790

Strany počet

8

URL

https://www.sciencedirect.com/science/article/pii/S2001037024000138?via%3Dihub

Plný text v Digitální knihovně

http://hdl.handle.net/11012/245285

BibTex

@article{BUT187210,
  author="Jana {Musilová} and Zdeněk {Vafek} and Bhanwar {Punyia} and Ralf {Zimmer} and Tomáš {Helikar} and Karel {Sedlář}",
  title="Augusta: From RNA-Seq to Gene Regulatory Networks and Boolean Models",
  journal="Computational and Structural Biotechnology Journal",
  year="2024",
  volume="23",
  number="December 2024",
  pages="783--790",
  doi="10.1016/j.csbj.2024.01.013",
  issn="2001-0370",
  url="https://www.sciencedirect.com/science/article/pii/S2001037024000138?via%3Dihub"
}