Fig. 5

Comparative analysis, Protein-protein interaction (PPI) network and functional enrichment network construction of top 200 DEmRNAs. a. The Circos plot showing how genes from the input gene lists overlap, in which on the outside the red arch represents the 58 unique differential genes reported by Hui Du et al., the blue arch representing 173 unique differential genes reported by Michael Costigan et al., and the green arch representing our top 200 unique differential genes; on the inside dark orange color represents the genes that appear in multiple lists and light orange color represents genes that are unique to that gene list; and purple lines link the same genes that are shared by multiple gene lists, blue lines linking the different genes where they fall into the same ontology term (the terms statistically significantly enriched and with size no larger than 100). b. PPI network constructed by the top 200 DEmRNA-coding protein. The color scale of the node indicates the number of connectivity with other nodes and the thickness of the edge indicates the combined score of the interaction. The clusters in light yellow frame were the top four subnetworks calculated by MCODE. c. Functional enrichment network constructed by nodes representing terms with the best p values from each of the 20 clusters, with the constraint that there are no more than 15 terms per cluster and no more than 250 terms in total and edges connecting terms with a similarity > 0.3