Fig. 1

Differential gene expression between periodontitis-affected and healthy gingival tissues. a A volcano plot shows the differentially expressed genes. Red dots represent the significantly up-regulated genes and blue dots stand for the significantly down-regulated genes in periodontitis-affected gingival tissues. The x-axis represents the log₂-transformed gene expression in periodontitis tissues (P) divided by that in healthy gingival tissues (H). The y-axis is the adjusted p value (−log₂) by Benjamini-Hochberg correction. b Protein functional classification in differentially expressed genes was performed using the PANTHER tool. The green arrows indicate protein functional classes that show significantly different composition (more than 7 % composition difference) between healthy and periodontitis tissues. c The expression of selected genes in RNA sequencing data was validated by a real-time RT-PCR analysis. The x-axis indicates the −ΔΔCt values and the y-axis represents log₂ (fold changes) obtained by RNA sequencing. The linear regression was performed with Pearson’s correlation coefficient (R) and the corresponding p value based on the gene expression values by both methods