Figure 3

Transcription factors (TFs) and immunity genes are enriched in the co-expression network of unstimulated macrophage. (a) BMDM associated basal homeostatic gene co-expression network (8357 nodes and 63,130 edges) with 17 significant modules. (b) The degree distribution of nodes in BMDM associated homeostatic gene co-expression network (r² = 0.92, Mann Whitney test P < 0.0001) and random network. Only 7.86% (657) of nodes have a high degree (Hub⁵⁰) representing the scale-free property of the co-expression network. (c) The relationship between connectivity and degree of nodes shows a significant positive correlation (r² = 0.82) suggesting the Hub⁵⁰ nodes and their modules are highly connected. (d) The distribution of genes and TFs (in percent) in represented modules with turquoise having a maximum 1205 (15.4%) genes and 22 TFs (20%, Hypergeometric enrichment test P < 0.05), and grey60 having minimum 186 genes (2.3%) and 4 TFs (3.63%) of all co-expressed genes/TFs. Also, TFs in purple and lightcyan modules are significantly enriched than genes assigned these modules (Hypergeometric test P < 0.01 and 0.05, respectively). (e) The average connectivity of all TFs is significantly higher (96.09) than the genes (93.02) in the co-expression network (Wilcoxon matched-pairs signed rank test P-value < 0.0001). (f) Immune-related genes form bicluster1 (Fig. 1e) are significantly enriched in Hub⁵⁰ (Hypergeometric enrichment test, P < 1.4e−29) representing their importance in the co-expression network.