Figure 1. WGCNA analysis identifies KL as the top IPF-relevant gene from the systems-level perspective. (A) Gene network modules from IPF patients and normal controls are well preserved, two of which (BROWN and BLUE) are significantly associated with IPF. The x axis represents preservation statistics for the corresponding module, and y axis shows the correlation between each module and the clinic trait. The size of each circle is proportional to the number of genes in each module. The horizontal line indicates the threshold for significant association between module and trait, while the vertical line for module preservation. (B) Network heatmap plot exhibits connectivity between genes of BROWN module. Higher co-expression relationship is indicated by red colors. Hub genes are positioned at the left-bottom corner as they display high connectivity with most of the remaining of the genes. The position of KL is specified. (C) Heatmap shows relative expression of 3544 genes in BROWN module. The expression of KL is specified by a dashed line. (D) Circular visualization of the results of gene annotation analysis shows enriched biological processes of BROWN module. The outer circle is a scatter plot showing the log fold change of the assigned genes for each process. The inner circle is a bar plot whose height is proportional to the extent of enrichment for each process. Filled colors corresponds to a z-score that is a crude measure of how likely the biological process is to be decreased or increased.