Summary of differentially expressed genes and enriched canonical pathways for each treatment.

(A,B) Venn diagram of differentially expressed genes in TGF-β1 and MTX-treated tissues relative to vehicle-treated control tissues for the standard (-KCs) versus modified (+KCs) tissue model at treatment day 14 and 28. (C,D) Enriched pathways from the list of differentially expressed genes observed in the standard tissue model for each treatment. (E,F) Enriched pathways from the list of differentially expressed genes observed in the modified tissue model for each treatment. Data represent the -log(P-value) for pathway significance (bars) and the ratio (black line) of the number of genes from the dataset divided by the total number of genes comprising a pathway from the IPA knowledge base. The shading within each bar represents the proportion of down (blue) versus upregulated (red) genes within a particular pathway. Abbreviations: AKT, serine-threonine protein kinase; FDR, false discovery rate; FXR, farnesoid X receptor; GADD45, growth arrest and DNA damage; LPS, lipopolysaccharide; LXR, liver X receptor; PI3K, phosphoinositide 3-kinase; PXR, pregnane X receptor; RXR, retinoid X receptor.