Benchmark Boolean Models for Gene Regulatory Networks

Ulm University

doi:10.5281/zenodo.17406798

Benchmark Boolean Models for Gene Regulatory Networks

Ulm University

Publisher: Zenodo
DOI: 10.5281/zenodo.17406798
Repository: zenodo.org
Language: en

Abstract

Gene regulatory networks (GRNs) capture the processes involved in gene regulation. Boolean network (BN) modeling provides a simple but effective framework for understanding the dynamical behavior of GRNs. Although BNs have been widely studied and applied, algorithms and theoretical analyses are usually tested on ad hoc models, which may introduce bias and fail to capture the properties of real GRNs. Benchmarking offers standardized models for validation and comparison. We construct benchmark BN models for GRNs of four major biological kingdoms: animals, bacteria, fungi, and plants. All models are built from empirically observed recurrent properties and motifs in GRNs. The proposed benchmark BNs provide a basis for evaluating algorithms and theoretical analyses.

Full text

Supplementary Material for Benchmark Boolean Models for Gene Regulatory Networks Caya L. O. Hotstegs1,∗, Jose P. Llano1,2,∗, Hans A. Kestler1,3 1Institute of Medical Systems Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany 2Department of Mathematics, University of Castilla-La Mancha, 02071 Albacete, Spain 3Leibniz Institute on Aging – Fritz Lipmann Institute, Beutenbergstraße 11, 07745 Jena, Germany ∗These authors contributed equally This PDF file includes: •Tables 1 to 4 (Attractor Analysis with BoolNet [1]). 1 1 Attractor Analysis Table 1: Type and number of attractors in the proposed benchmark Boolean network models for the animal kingdom. OR-NOT AND-OR-NOT General canalizing Type Number Fixed point 4 ∗ ∗ ∗ ∗ Type Number ∗ ∗ 2-periodic 2 ∗ ∗ Type Number Fixed point 2 2-periodic 2 4-periodic 4 Table 2: Type and number of attractors in the proposed benchmark Boolean network models for the bacteria kingdom. OR-NOT AND-OR-NOT General canalizing Type Number Fixed point 2 ∗ ∗ Type Number Fixed point 6 ∗ ∗ Type Number Fixed point 10 2-periodic 4 Table 3: Type and number of attractors in the proposed benchmark Boolean network models for the fungi kingdom. OR-NOT AND-OR-NOT General canalizing Type Number Fixed point 6 ∗ ∗ ∗ ∗ Type Number Fixed point 2 2-periodic 4 ∗ ∗ Type Number Fixed point 5 ∗ ∗ 3-periodic 8 Table 4: Type and number of attractors in the proposed benchmark Boolean network models for the plants kingdom. OR-NOT AND-OR-NOT General canalizing Type Number Fixed point 2 Type Number Fixed point 6 Type Number Fixed point 6 2 References [1] M¨ussel, C., Hopfensitz, K. & Kestler H. A. BoolNet–an R package for generation, reconstruction and analysis of Boolean networks. Bioinformatics 26(10), 1378–1380, https://doi.org/10.1093/bioinformatics/btq124 (2010). 3