Figure 9
Relative abundance of differentially expressed proteins and functional clusters related with cellular protein metabolic process and pentose biosynthesis process during the differentiation developmental stage (day 8 vs day 12) in a gilthead sea bream primary muscle cell culture. On the top, the network analysis of protein-protein interactions among proteins grouped into four functional categories, according to Gene Ontology enrichment analysis by GOEAST. In these networks, nodes are proteins, the thickness of the line indicate the degree of confidence prediction of the interaction, according to the STRING databases66. On the bottom, the relative abundance of protein spots of each cluster are showed. Data are shown as mean ± SEM of % vol. Significant differences by t-test (p < 0.05). The average of local clustering coefficients were 0.79 for “Cellular protein metabolic process” (GO: 0044267, p = 4.95e-05), which grouped two clusters: “Cellular amino acid metabolic process” (GO: 0006520, p = 6.75e-05) and “Regulation of cellular aa metabolic process” (GO: 0006521, p = 1.41e-07, clustering coefficient = 1), and “pentose biosynthesis process” (GO: 0019322, p = 0.000395, clustering coefficient = 1). Protein acronyms correspond to Gene Symbol (see Supplementary Table S2 for details).The interactome of differentiation phase is represented in Fig. 6B, and more relevant data from the network stats are provided in Supplementary information (Table S4).
