Review and assessment of Boolean approaches for inference of gene regulatory networks

Pušnik, Žiga (author), Mraz, Miha (author), Zimic, Nikolaj (author), Moškon, Miha (author)

Boolean descriptions of gene regulatory networks can provide an insight into interactions between genes. Boolean networks hold predictive power, are easy to understand, and can be used to simulate the observed networks in different scenarios. We review fundamental and state-of-the-art methods for inference of Boolean networks. We introduce a methodology for a straightforward evaluation of Boolean inference approaches based on the generation of evaluation datasets, application of selected inference methods, and evaluation of performance measures to guide the selection of the best method for a given inference problem. We demonstrate this procedure on inference methods REVEAL (REVerse Engineering ALgorithm), Best-Fit Extension, MIBNI (Mutual Informationbased Boolean Network Inference), GABNI (Genetic Algorithm-based Boolean Network Inference) and ATEN (AND/OR Tree ENsemble algorithm), which infers Boolean descriptions of gene regulatory networks from discretised time series data. Boolean inference approaches tend to perform better in terms of dynamic accuracy, and slightly worse in terms of structural correctness. We believe that the proposed methodology and provided guidelines will help researchers to develop Boolean inference approaches with a good predictive capability while maintaining structural correctness and biological relevance.

• Language: English
• Keywords: Boolean network inference, gene regulatory networks, static validation, dynamic validation, systems biology
• Work type: Article
• Typology: 1.02 - Review Article
• Organization: FRI - Faculty of Computer and Information Science
• Publication status: Published
• Publication version: Version of Record
• Year: 2022
• Number of pages: 15 str.
• Numbering: Vol. 8, iss. 8, art. e10222
• PID: 20.500.12556/RUL-139693
• UDC: 004:575.112
• ISSN on article: 2405-8440
• DOI: 10.1016/j.heliyon.2022.e10222
• COBISS.SI-ID: 117893635
• Publication date in RUL: 06.09.2022

Record is a part of a journal

• Title: Heliyon
• Publisher: Elsevier
• ISSN: 2405-8440
• COBISS.SI-ID: 21607432

Licences

• License: CC BY-NC-ND 4.0, Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
• Link: http://creativecommons.org/licenses/by-nc-nd/4.0/
• Description: The most restrictive Creative Commons license. This only allows people to download and share the work for no commercial gain and for no other purposes.

Secondary language

• Language: Slovenian
• Keywords: inferenca Boolovih mrež, gensko regulatorna omrežja, statična validacija, dinamična validacija, sistemska biologija