Figure 6

Analysis of the “overlap” of development-related gene expression between different tissues. A) Venn Diagram showing overlap of development-related gene expression in five different human types of tissue (peripheral blood mononuclear cells, conjunctival epithelia, temporal lobe brain, quadriceps muscle and bone marrow) [ANOVA, p < 0.05], overlap of three or more data sets shown as darker shade. B) Interactome network (Biogrid 3.1.87) model inferred from overlapping genes with development-related expression in ≥3 out of 5 different types of human tissue, protein connectivity (degree) is represented by colour gradation of nodes, dark red = high degree to blue = low degree, as defined by the Cytohubba Cytoscape plugin (426 protein nodes, 447 connections). C) Tissue-independent minimal essential network (MEN) derived from genes with development-dependent gene expression. The minimal essential network was constructed using genes within the top 10% score for “degree” and “bottleneck” derived from an interactome network (Biogrid 3.1.87) model inferred from overlapping genes with development-related expression in >3 out of 5 different types of human tissue (peripheral blood mononuclear cells, conjunctival epithelia, temporal lobe brain, quadriceps muscle and bone marrow). A minimal essential network is a marker of functionally relevant biological pathways [15, 16], modularity within the MEN was assessed using spectral partition based network clustering [37], the three modules identified are coloured blue, green and pink. Network edges are as follows; “->” for activating/catalyzing, “-|” for inhibition, “- -” for functional interactions extracted from complexes or inputs, and “---” for predicted functional interactions. D) Evolutionarily conserved growth pathways identified in the main data set also overlap with the minimal network constructed from the intersection of development-related gene expression in different human tissue. Biological pathways were identified by network module with the Reactome Cytoscape plugin using the Hypergeometric test with false discovery rate modified p-value (FDR).