Differentially expressed genes.
The analysis of DE genes between the 100μg DNA IM group and 50μg DNA EP group was shown in Figure 3. The concordance rates of down-regulated and up-regulated DE genes between the two groups were 56.9% and 53.2%, respectively. First, we screened out the top 20 up-regulated DE genes and down-regulated DE genes in the 100μg DNA IM group, and then counted the differential expression levels of these DE genes in the TB model group and 50μg DNA EP group (Supplementary Table 1, 2). Second, we screened out the top 20 up-regulated DE genes and down-regulated DE genes in the 50μg EP group, and then collected the differential expression levels of these DE genes in the TB model group and 100μg DNA IM group (Supplementary Table 3, 4). Finally, we compared the consistency of DE genes in four tables to analyze the commonality of the action targets of the two vaccination methods (IM and EP) in the mouse TB model. The results showed that: (1) Of the top 20 down-regulated and the top 20 up-regulated DE genes in the 100μg DNA IM group and 50μg DNA EP group, 18 (81.8%) down-regulated DE genes and 13 (48.1%) up-regulated DE genes between the two groups were the same. (2) Most of the DE genes significantly down-regulated in the 100μg DNA IM group and 50μg DNA EP group were related to the digestion and absorption of nutrients or neuroendocrine, for example, dysfunction of the pancreatic island (Iapp, Scg2, Chga, Chgb), metabolism of carbohydrate and glycogen (Amy2a5, Gcg, Ins1), protein hydrolysis (Try5, Cpa1, Gm13011, Try4, Cpb1), lipid metabolism (Ins1, Pnlip), neuroendocrine (Vstm2l, Resp18), etc. Most of the significantly up-regulated DE genes were related to the cellular structural proteins and cellular functional proteins, in which alveolar cell structure and function proteins account for a large proportion, for example, Sftpc, Sftpc, Sftpb, Sftpd, Sftpa1, Wfdc2, Sec14l3, Postn, Cldn5, Aqp5, Emp2, and Foxf1, etc. (3) The expressions of the top 20 DE genes in 100μg DNA IM group and 50μg DNA EP group, whether up-regulated or down-regulated, were opposite to those in the TB model group.