Fig. 4

Gene Ontology (GO) enrichment analysis of the differentially expressed genes in the neuronal cells. GO enrichment analysis was performed using the enriched and the depleted genes from the neuronal cells. Figures illustrate a subset of GO terms common to both the neuronal and non-neuronal population biological properties hierarchies (see Additional files 9 and 18 for complete hierarchies, the interactive hierarchies can be obtained from the BioGRID repository) and a few specific to one or the other hierarchy (a) and (b). The hierarchies of the GO terms are based on the number of genes and the significance for the category biological process (compare to Table 1). The circles/nodes represent the different GO terms, where the size of the circle represent the number of genes associated with the term, i.e., the larger the circles, the more the number of genes associated with the GO term. The color scheme represents the significance: white represents the least, and orange represents the most significant terms. The white, yellow and orange circles represent the terms common to both the neuronal and non-neuronal networks, while the red and blue circumferences of the circles represent terms specific to either the neuronal or non-neuronal data sets respectively. a Core hierarchy of GO terms defining biological processes in enriched genes comprising the ‘neuronal’ gene set. 530 genes are included in this analysis. b. Core hierarchy of GO terms defining biological processes in the depleted genes comprising the ‘non-neuronal’ gene set. 482 genes are included in this analysis. The green and pink boxes highlight examples of sub hierarchies within the larger hierarchies of biological process GO terms common to both populations but differentially enriched between the two. Sub-hierarchies of biological process GO terms are significantly enriched in the neuronal population, ‘ion transport’ and ‘nervous system development’ but not in the non-neuronal population (shaded pink boxes). Examples of GO term sub-hierarchies enriched in the non-neuronal population include regulation of ‘metabolic and biosynthetic processes’ and ‘organ development’ (shaded green boxes). The corresponding p-values and percentage of genes associated with the GO terms in the green and pink boxes as well as the specific terms in either population are shown in Table 1