Fig. 2

Summary of bulk RNA-seq data pre-alignment day (day 0, the day prednisone treatment was initiated in patients with PF). a Depicts an overview of the complete cohort and general workflow per data set (dashed: pre-alignment day data set; solid: post-alignment day data set). b Shows the expression profile across the time points prior to the alignment day per module in a heatmap split by condition. The amount of samples per timepoint is displayed in brackets. Tiles are colored based on the group fold change (GFC) and modules are represented by their respective colors. Percentage of LMEM genes per module are depicted in a barplot (colored based on significance in the LMEM) and total numbers are shown as a ratio of LMEM genes to module genes. c Displays the mean expression per fibrosis-related module filtered by the LMEM genes over time prior to the alignment day. Lines and confidence intervals are colored according to the condition. d Depicts the mean expression of the top 10 LMEM genes per fibrosis-related module ordered by effect size for all conditions and time points prior to the alignment day. Modules are colored accordingly and effect size is indicated by the dot size. e Shows significant representative functional enrichment terms from GO and KEGG database as well as the hallmark gene set of the Molecular Signature Database per fibrosis-related module. Modules names are displayed on the x-axis and the respectively colored squares indicate the enrichment of a functional term in the module. f Displays the Kaplan–Meier plot of patients with idiopathic pulmonary fibrosis with and without enrichment of genes in the maroon module. Lines are colored based on the enrichment of the LMEM genes in the maroon module in the reference dataset using GSVA