Three topological features of regulatory networks control life-essential and specialized subsystems

• Autor(es): Wolf, Ivan Rodrigo [UNESP] ; Simões, Rafael Plana [UNESP] ; Valente, Guilherme Targino [UNESP]
• Data: 2022
• Identificador Persistente: http://hdl.handle.net/11449/223091
• Origem: Oasisbr
• Tipo de Documento: Artigo científico
• Idioma: Inglês

Descrição

Made available in DSpace on 2022-04-28T19:48:30Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-12-01

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Gene regulatory networks (GRNs) play key roles in development, phenotype plasticity, and evolution. Although graph theory has been used to explore GRNs, associations amongst topological features, transcription factors (TFs), and systems essentiality are poorly understood. Here we sought the relationship amongst the main GRN topological features that influence the control of essential and specific subsystems. We found that the Knn, page rank, and degree are the most relevant GRN features: the ones are conserved along the evolution and are also relevant in pluripotent cells. Interestingly, life-essential subsystems are governed mainly by TFs with intermediary Knn and high page rank or degree, whereas specialized subsystems are mainly regulated by TFs with low Knn. Hence, we suggest that the high probability of TFs be toured by a random signal, and the high probability of the signal propagation to target genes ensures the life-essential subsystems’ robustness. Gene/genome duplication is the main evolutionary process to rise Knn as the most relevant feature. Herein, we shed light on unexplored topological GRN features to assess how they are related to subsystems and how the duplications shaped the regulatory systems along the evolution. The classification model generated can be found here: https://github.com/ivanrwolf/NoC/.

Department of Bioprocess and Biotechnology School of Agriculture São Paulo State University (UNESP)

Medical School Sao Paulo State University (UNESP)

Max-Planck-Institut für Herz- und Lungenforschung Max Planck Institute

Department of Bioprocess and Biotechnology School of Agriculture São Paulo State University (UNESP)

Medical School Sao Paulo State University (UNESP)

FAPESP: 2015/12093-9

FAPESP: 2015/19211-7