Fig. 3

Co-expression of protein-coding genes and long non-coding RNAs within functional modules identified by WGCNA at the pre-pregnancy baseline. Using the gene-level counts from the RA_improved, RA_worsened and healthy women at the pre-pregnancy baseline, weighted gene co-expression network analysis (WGCNA) identified 27 modules of coding genes and lncRNAs with highly correlated intra-module expression. The different modules (with color labels) are shown on the left. For each module, the five columns to the right indicate, in respective order, (1) the correlation between module eigengene expression and subsequent improvement/worsening during pregnancy (RA group), (2) total number of genes (among all genes analyzed) that clustered within the module, (3) the number of genes (coding/lncRNAs) differentially expressed between the two RA groups that are co-expressed within the module, (4) fold enrichment of these differentially expressed genes within the module, and (5) the FDR value for the enrichment analysis. The midnightblue, light yellow, and salmon modules were significantly enriched in genes differentially expressed between the RA_improved and RA_worsened groups, and their eigengene expression patterns were significantly correlated with subsequent improvement or worsening of RA during pregnancy. The grey module represents genes that were not co-expressed and were not assigned to any of the co-expression modules