Chapter 3 78 Next, we wanted to infer a gene regulatory network using our data. We used Maximum Clique Centrality (MCC) to calculate MCC, a centrality measure, to identify the most central or influential nodes (in this case, genes) in a network. It is based on the concept of cliques, which are subsets of nodes in a network that are fully connected to each other (i.e., all nodes within the subset are directly connected). A hub gene is a gene within a biological network (e.g., a gene interaction network or a protein-protein interaction network) that has a high degree of connectivity (Chin et al., 2014). We identified a set of central hub genes based on their connectivity and associated centrality scores (Figure 3.15, Table S3.4 in digital supplement). We looked at the behavior of the hub genes in response to FR and observed a notable downregulation of several of them at 6h internode (Figure 3.16). Among these genes are Solyc02g031900 (kinase family protein), Solyc02g031970 (encoding 50S ribosomal protein L12-2 localized to the chloroplast), Solyc03g118150 (Sec14-like), a gene potentially involved in cellular retinaldehyde-binding or triple function, Solyc06g071370 (NHL repeat-containing protein-like gene), Solyc07g041930, (Adenylyl cyclase) and Solyc10g005100 (Salt stress root protein RS1). The downregulated hub genes may play integral roles in the plant’s response to FR light, potentially affecting processes related to kinase activity, ribosomal function, cellular retinaldehyde binding, and stress responses. Figure 3.15. Hub genes and their centrality. The color gradient indicates the Maximum Clique Centrality (MCC) score. MCC calculates the size of the largest clique that a node belongs to and assigns a centrality score based on this. The score is indication of the centrality which is represented by the redness of the color.
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