Figure 3

Aberrant profile of the S100A4 knockout lens transcriptome. (A) Two-dimensional plot of the principal component (PC) analysis for RNA-seq data of S100A4^−/− (red) and littermate WT (green) mouse lenses (n = 2; for each sample 6–12 lenses were pooled derived from P30 mice. The X axis and Y axis depict the PC1 and PC2, respectively. The value after the PC identifier displays the proportion of variance. (B) Heat map of expression values of differentially expressed genes in S100A4^−/− lenses compared to littermate WT lenses. Only differentially expressed genes (≥ twofold difference in expression, adjusted P value of ≤ 0.05) were used for creating the heat map. Each column corresponds to one sample, and each row corresponds to a gene. The genes are hierarchically clustered using a correlation distance with complete linkage and show the similarity of their expression profiles between S100A4^−/− and littermate WT samples. (C) The volcano plot showcasing the results of the comparison between S100A4^−/− and littermate WT samples. The log2-fold changes which were calculated based on S100A4^−/− /WT were plotted on the x-axis. The − log10 p-values are plotted on the y axis. Each dot represents a gene. (D,E) Gene enrichment analysis of differentially expressed genes in S100A4^−/− mouse lens. Gene enrichment analysis was performed using the Molecular Signatures Database (MSigDB) using the results of the comparison of genes in S100A4^−/− lenses compared to WT lenses. The top 20 most significantly enriched GO terms (D) and KEGG curated pathways (E) were illustrated by their normalized enrichment score. Red and blue bars show proportional upregulated and downregulated genes in a given pathway, respectively.