Fig. 3

Direct comparison of gene expression between RNA-Seq (FFPE) and microarray data (FF). a Microarray Log₂(FC) IPF vs control was plotted on x axis and RNA-Seq Log₂(FC) IPF vs control was plotted on y axis. Yellow dots indicate common increased genes, purple dots indicate common decreased genes, grey dots indicate genes with discordant patterns of differential expression and white dots indicate genes that are not significantly differentially expressed genes in both datasets or not significant in microarray and significant in RNA-Seq and vice versa. b Venn diagram colored in yellow indicates gene overlap between increased genes in RNA-Seq and microarray. 760 represents commonly increased genes, 940 is a number of genes that is increased in RNA-Seq data and do not overlap with microarrays while 1,546 is a number of increased genes in microarrays that do not overlap with RNA-Seq (FDR adjusted p < 0.05). Venn diagram colored in purple represents overlap between of decreased genes in both sets (FDR adjusted p < 0.05) and it follows the same logical relations as a Venn diagram in yellow