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

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

Povzetek

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.

Ključne besede

inferenca Booleovih mrež;gensko regulatorna omrežja;statična validacija;dinamična validacija;sistemska biologija;Boolean network inference;gene regulatory networks;static validation;dynamic validation;systems biology;

Podatki

Jezik:	Angleški jezik
Leto izida:	2022
Tipologija:	1.02 - Pregledni znanstveni članek
Organizacija:	UL FRI - Fakulteta za računalništvo in informatiko
UDK:	004:575.112
COBISS:	117893635
ISSN:	2405-8440
Št. ogledov:	33
Št. prenosov:	18
Ocena:	0 (0 glasov)
Metapodatki:

Ostali podatki

Sekundarni jezik:	Slovenski jezik
Sekundarne ključne besede:	inferenca Boolovih mrež;gensko regulatorna omrežja;statična validacija;dinamična validacija;sistemska biologija;
Vrsta dela (COBISS):	Članek v reviji
Strani:	str. 1-21
Letnik:	ǂVol. ǂ
Zvezek:	ǂno. ǂ
Čas izdaje:	2022
DOI:	10.1016/j.heliyon.2022.e10222
ID:	16382214