Microarray experimental design and volcano plots displaying differential expression between TNFα-treated and control cells. (A) For each of the three gingival fibroblast cell lines, cells were treated with TNFα (20 ng/ml) or cultured without TNFα for 1, 3 or 6 h. Samples were labeled and hybridized on oligonucleotide microarrays. Each arrow corresponds to one hybridization where the green sample is labeled with Cy3 and the red sample with Cy5. (B-D) The y axis displays the negative false discovery rate (-FDR) on a log10 scale and the x axis displays the M-value which is the log2 of the ratio gene expression of TNFα treated cells/gene expression of control cells. A positive M-value corresponds to higher expression in the TNFα treated cells. The vertical line signifies a false discovery rate of 0.05, and all genes above it are considered differentially expressed. (B) At time point 1 h, 1157 genes were differentially expressed in response to TNFα. For (C) and (D), the differentially expressed genes at the later time point were compared with the differentially expressed genes at the earlier time point, to retrieve the genes that were differentially expressed due to time and treatment between those time points. (C) Between time points 1 h and 3 h, 796 genes were differentially regulated due to TNFα treatment. (D) Between time points 3 h and 6 h, 553 genes were differentially regulated due to TNFα treatment.