PMC

The royalblue module was visualised according to a prefuse force directed layout based on weighted correlations between genes. Minor manual changes to node placement were made to maximise clarity. The size of each node (and node label) reflects absolute module membership (MM) values, with larger nodes corresponding to higher MM values. Node colour indicates whether royalblue genes were encoded by autosomal (azure), X chromosome (purple), or mitochondrial (red) DNA. Edge width reflects the weighting of connections between nodes, with thicker edges corresponding to stronger connections

PPI network analysis of POSTN in the royalblue module. (A) PPI network analysis of genes in the royalblue module. (B,C) Top 15 genes in the royalblue module identified by the stress (B) and betweenness (C) algorithms in cytoHubba.

Relationship between key modules and clinical features and GO analysis of genes in the key module. (A,B) Scatterplots of GS vs. MM in the royalblue module with creatinine and eGFR of IgAN patients. The correlation between GS and creatinine and eGFR was 0.53 (P = 1.2e−08) and 0.21 (P = 0.035), respectively. POSTN had the highest MM and GS for creatinine (MM = 0.82 and GS = 0.66) and eGFR (MM = 0.82 and GS = −0.67) of all genes in the royalblue module. (C) Heatmap and bar graph of gene expression distribution of 101 genes in the royalblue module. (D) GO analysis of genes in the royalblue module, with threshold count ≥2 and P < 0.05. (E) Only one KEGG pathway (protein digestion and absorption) was enriched for the royalblue module; three additional pathways (ECM–receptor interaction, focal adhesion, and amoebiasis) are shown.

Green colour indicates reduced gene expression in better lithium treatment responders, relative to poor responders. Red colour indicates increased gene expression, respectively. The mitochondrial complex 1 is identified as the central functional hub within the royalblue module