Paths Through the Yeast Regulatory Network in Different Physiological States. Issue 21 (15th October 2021)

• Record Type: Journal Article
• Authors: Lesk, Arthur M.; Konagurthu, Arun S.
• Is Part Of: Journal of molecular biology. Volume 433:Issue 21(2021)
• Publication Date: 2021-10-15
• Subjects: regulatory networks -- pathway analysis and comparison -- systems biology; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2021.167181
• Languages: English
• ISSNs: 0022-2836

Abstract

Graphical abstract: Highlights: We enumerate and analyse paths through Yeast gene-expression regulatory networks. Comparing five states reveals shared and different aspects of node and edge usage. The networks use overlapping sets of nodes and edges but assemble them independently. The cell-cycle network is an outlier in terms of density of pathways. The results show details of the mechanisms of reprogramming the networks. Abstract: We analyse paths through the regulatory networks that control gene-expression patterns in Yeast, in five different physiological states: cell cycle, DNA damage, stress response, diauxic shift, and sporulation. The network in each state is specified as a directed graph, containing different sets of edges connecting pairs selected from a combined set of 1475 nodes. Each network contains some nodes that have no parents, and others that have no children. We call these, respectively, 'source' and 'sink' nodes. For each network we enumerate paths between source and sink nodes. In a previous paper (Lesk and Konagurthu, 2020), we defined, extracted and compared the neighbourhoods of each transcription factor in different physiological states, and how the system reconfigures itself. Here we compare the usage of nodes and edges by different networks, and how they are assembled into paths. The picture that emerges is that the networks are not disjoint but show substantial sharing of nodes and edges; however, they assemble these materials into different sets of paths. Four of the networks, other than the cell-cycle network, contain paths between only a small fraction ( < 13%) of possible source-sink pairs. Although the cell-cycle network is not an outlier in terms of total number of nodes and edges, and number of sink nodes, it is very much an outlier in having a greater proportion of source-to-sink paths than the other networks.