Fig. 3
From: PARK2 as a susceptibility factor for nontuberculous mycobacterial pulmonary disease
Protein-protein interaction analysis of NTM-PD. (A) Co-expression protein network construction. Red nodes represent significantly upregulated genes; blue nodes represent significantly downregulated genes. The nodes denote the number of proteins, while the edges represent their interactions. Node size is inversely related to the P value; edge color and edge width are directly related to the confidence score. (B) Modules of protein-protein interaction networks. The molecular complex detection (MCODE) plugin of Cytoscape was used for the analysis. The cluster finding parameters included a degree cutoff of 2 to exclude loops, a node score cutoff of 0.2, a kappa score of 2, and a max depth of 100, which limits the cluster size for co-expressing networks. Node shapes indicate the cluster status of the nodes. A square represents the seed (highest scoring rnode in the cluster), and a circle represents clustered proteins. Node color represents the node score; a range from black to red indicates the MCODE computed node scores (lowest to highest, respectively)