Figure 2. Subtractive analysis of MTEC microarray data.

(A) Experimental flowchart detailing microarray analysis. (B) The number of differentially expressed genes in ciliated MTECs at adj. p-values <0.05, <0.01 and <0.001 before subtraction (non-subtracted) and after subtraction. The non-subtracted gene list is the transcriptional profile of GFP+ cells compared to a universal mouse reference RNA. The subtracted gene list was derived analytically by comparing the transcriptional profile of GFP+ cells to that of GFP- cells from MTEC cultures. The number of genes that show 2-fold or greater differential expression and have adjusted p-values of 0.05, 0.01 and 0.001 are shown before and after subtractive analysis. After subtraction, 649 genes were significantly upregulated at ALI+4 with respect to GFP- cells, and 73 genes at ALI+12. 143 genes were downregulated at ALI+4 and none at ALI+12 (adj. p<0.05). (C) The overlap of significantly upregulated and downregulated genes (adj. p<0.05) from ALI+4, ALI+12 and GFP- pools decreases after subtraction. The GFP- group in both panels represents genes that are differentially expressed in non-ciliated cells relative to the universal reference RNA. M = log₂(fold change).