Ut that general health differences might have some effect on the final outcome. However, the 
comparison of the gene expression profiles of all individuals should minimize potential interfering signals originating from single individuals affected with other diseases. Our RNA-Seq analysis, investigating the gene expression profile in the gingival tissues showed that the genes were differentially distributed between healthy and periodontitis-affected samples. Enrichment analysis among uniquely expressed genes in the periodontitis-affected tissues showed regulated pathways indicative of inflammation, such as 1948-33-0 site cytokine signaling, chemokine signaling and the JAK-STAT signaling pathway. Several cytokines such as interleukins, which are involved in periodontits, signal through the JAK-STAT signaling pathway [33]. On the other hand, in the healthy biopsies, pathways were indicative of non-inflammatoryprocesses that may be involved in the maintenance of the healthy gingival tissue. Future studies should also include investigation of genes within these pathways, which may contribute to understanding, prevention and treatment of periodontitis. Differential gene expression analyses of periodontitis-affected vs. healthy gingival tissues showed the majority of differentially expressed genes to be upregulated in the periodontitis-affected tissues. Furthermore, GO enrichment analysis among these differentially expressed genes demonstrated that most of these genes were involved in immune and inflammatory processes. This is in line with the increased inflammatory response in the tissue, and also in accordance with our previous microarray studies on inflammatory-stimulated cell cultures reporting that gene expression profiles of TNFa-stimulated cells show an induction of inflammatory genes [34,35]. Up to date, RNA-Seq studies aimed to identify new genes involved in the Tunicamycin web pathogenesis of periodontits have not been reported. One ab initio study by Covani et al. [36] identified genes with potential roles in periodontitis, some of which have not previously been associated with the disease. However, the protein expression of these genes in periodontitis-affected tissues has not been confirmed. In our study we aimed to identify genes involved in the pathogenesis of periodontitis. Therefore, we further searched through the differentially expressed genes, focusing on the top 50 upregulated genes. Two of these 50 upregulated genes, IRF4 and CCL18, were also detected at the protein level in periodontitis affected-tissues, supporting these genes as novel finds in the pathogenesis of periodontitis. Furthermore, these two selected genes have been reported to be involved in other chronic inflammatory diseases such as RA. The transcription factor, IRF4, has been demonstrated to be involved in T-cell-dependent chronic inflammatory diseases such as IBD [37]. Mudter et al. 2011 reported a correlation between mRNA levels of IRF4 and production of cytokines such as IL-6 and IL-17 in the inflamed colon from patients with IBD, indicating that IRF4 is involved in the regulation of chronic mucosal inflammation [37]. In addition, the gene for CCL18 was upregulated in periodontitis-affectedGene Expression in Periodontitisgingival tissues. This chemokine, expressed by macrophages, monocytes and dendritic cells, has been demonstrated to be increased in synovial tissue of RA patients [38]. It has also been suggested that blockage of CCL18 expression by anti-TNF-a antibodies identifies CC.Ut that general health differences might have some effect on the final outcome. However, the comparison of the gene expression profiles of all individuals should minimize potential interfering signals originating from single individuals affected with other diseases. Our RNA-Seq analysis, investigating the gene expression profile in the gingival tissues showed that the genes were differentially distributed between healthy and periodontitis-affected samples. Enrichment analysis among uniquely expressed genes in the periodontitis-affected tissues showed regulated pathways indicative of inflammation, such as cytokine signaling, chemokine signaling and the JAK-STAT signaling pathway. Several cytokines such as interleukins, which are involved in periodontits, signal through the JAK-STAT signaling pathway [33]. On the other hand, in the healthy biopsies, pathways were indicative of non-inflammatoryprocesses that may be involved in the maintenance of the healthy gingival tissue. Future studies should also include investigation of genes within these pathways, which may contribute to understanding, prevention and treatment of periodontitis. Differential gene expression analyses of periodontitis-affected vs. healthy gingival tissues showed the majority of differentially expressed genes to be upregulated in the periodontitis-affected tissues. Furthermore, GO enrichment analysis among these differentially expressed genes demonstrated that most of these genes were involved in immune and inflammatory processes. This is in line with the increased inflammatory response in the tissue, and also in accordance with our previous microarray studies on inflammatory-stimulated cell cultures reporting that gene expression profiles of TNFa-stimulated cells show an induction of inflammatory genes [34,35]. Up to date, RNA-Seq studies aimed to identify new genes involved in the pathogenesis of periodontits have not been reported. One ab initio study by Covani et al. 
[36] identified genes with potential roles in periodontitis, some of which have not previously been associated with the disease. However, the protein expression of these genes in periodontitis-affected tissues has not been confirmed. In our study we aimed to identify genes involved in the pathogenesis of periodontitis. Therefore, we further searched through the differentially expressed genes, focusing on the top 50 upregulated genes. Two of these 50 upregulated genes, IRF4 and CCL18, were also detected at the protein level in periodontitis affected-tissues, supporting these genes as novel finds in the pathogenesis of periodontitis. Furthermore, these two selected genes have been reported to be involved in other chronic inflammatory diseases such as RA. The transcription factor, IRF4, has been demonstrated to be involved in T-cell-dependent chronic inflammatory diseases such as IBD [37]. Mudter et al. 2011 reported a correlation between mRNA levels of IRF4 and production of cytokines such as IL-6 and IL-17 in the inflamed colon from patients with IBD, indicating that IRF4 is involved in the regulation of chronic mucosal inflammation [37]. In addition, the gene for CCL18 was upregulated in periodontitis-affectedGene Expression in Periodontitisgingival tissues. This chemokine, expressed by macrophages, monocytes and dendritic cells, has been demonstrated to be increased in synovial tissue of RA patients [38]. It has also been suggested that blockage of CCL18 expression by anti-TNF-a antibodies identifies CC.
